The first time a player finds this explosive egg there is nothing that tells the player that it is meant to dissolve that organic net. The player doesn't even get a clue that the egg explodes when you shoot it. The player has to find that out by trial and error. After the first time it becomes obvious the purpose of that egg, but the first time is not. That mistake repeats on the whole game. There are many obstacles that the player is left by their selves to solve. There are many objectives that the player isn't told that it is an objective in the first place. If the game tells the player that they must go to a building, it's natural for the player to look for a way to the building. If the game doesn't tell the player what to do nor where to go, how is the player supposed to guess the developer's intentions?

When  the player reaches this dimensional portal, the gravity on the other side seems to be correct. However, as soon as the player crosses the portal, gravity is reversed and the player is standing on the ceiling. The fact that the image does not match the gravity is probably a clue left by whoever made this puzzle. The game is not even consistent with itself because the first portal is the only one that has gravity not matching the image that you see of the other side. The first thing that the player sees is a locked door and nothing tells the player that they are in fact facing a puzzle. The secret of the puzzle is that you have to cross the portals in the room in a specific order, such that you end up walking on the floor with gravity correctly oriented. The game never explains why the door can only be opened if the player is standing on the floor, there isn't a button or anything that explains it. A simple button that could only be pressed or reached with the player standing on the floor would be enough to both tell the player that the room is a puzzle and would explain why the door doesn't open when the player is walking on the ceiling.

Nothing in the game tells that that blue glowing device shifts gravity when the player shoots it. The best that the game does is to give a hint about a gravity experiment or test. That blue device doesn't look like a target nor has any clues about shooting at it. The player has to find out by trial and error. After the first time the next time the player sees the same device they already know what to do. If the device is on the ceiling, gravity should reverse upside down. If the device is on a wall, shooting it shifts gravity in that direction.

Despite the intuitive behaviour of the blue devices, after the first time, the game doesn't obey its own rules. In some places the aliens are walking on walls or ceiling after the player has shifted gravity in another direction. Gravity should be an universal force for everyone in the same space but that's not the case in many places. In the case of the anti-gravity tracks the track is the excuse to disobey gravity. It's completely illogical for enemies to spawn through portals on walls or ceilings while the player is on the floor or vice-versa.

It also worth to mention that the first time the player encounters the blue devices has a slightly misleading scenario. The level has some devices that charge the plasma gun right before encountering the gravity device. An obvious association is that the plasma gun should be used to activate the blue device. That is true but that device can also be activated by means of any weapon fire. The game is misleading in many other cases, presenting the player with puzzles or challenges where it defies intuition and misleads the player's actions.

Another mistake related to gravity is that the water drops are a pre rendered animation. When the player shifts gravity upside down the animated water drops keep the same orientation, which disobeys the gravity shift. It'd had been pretty easy to fix it, just change the direction of the animation to match the direction of the gravity.

When the player finds a shuttle for the first time nothing is explained. The shuttle has a tractor beam to drag objects around but the player has to guess the beam's function. Right after boarding the first shuttle there are some objects intended to block the way. The objects don't prevent the player from opening the door and  the door itself isn't clearly shown to be a door. The game does highlight the objects with a blue tint but it's so subtle that the player can barely notice it. The cross-hair turns red when a valid target is found but the player still has to guess what is valid and what isn't a valid target.

When the player reaches this point there is nothing telling the player about what to do and where to go. What catches the player's attention is the wind tunnel with energy beams. The strong air flow blocks the player. What do you do? The first thing to notice is that one of the energy beams is offline and that red lights signal that the way is blocked. Whoever made this level was probably thinking "If the player sees that there are energy beams online, a fan spinning and one of the beams if offline. Then they should deduce that they should turn off the remaining beams". That prediction could have worked if the game presented clues to reason in that direction, but the game fails to do so. The developer's logic is contradictory in regards to signalling to the players what they have to do. Turning the beams also turns off the wind that is blocking the way, but the red lights change to blue when the player turns off the beams. Shouldn't light turn off instead of changing its color?

The trick in this area is to turn all energy beams off to pass. Turn off how? When the player lands on one of the landing pads with no forcefield the control panels are all offline and the doors won't open. The forcefields in this area should be a trivial obstacle as the player has already learned, in previous levels, that spirit walking solves it. By inspecting the control panels closely the player should notice that one of them opens up a lid where the energy beam is. Behind the lid there is a destructible metallic plate that the player has to guess that is destructible. After that the player has to guess that the shuttle's tractor beam has to be used to remove what seems to be an electrical fuse to turn the beam off.

In the previous challenge the player was tasked to turn the energy off to pass. In the next area the game contradicts itself. There are electrical arcs and a closed door with red lights on. It's natural for the player to think that the way to open the door is to somehow turn off the energy, as it was the case in the previous area. However, there is nothing to turn off in this next area. The metallic objects that are blocking the door should be moved for the door to open.

The game lacks cohesion with itself here. It feels like two different persons worked on the same level but they didn't talk to each other. The red lights signal a closed door and the player naturally looks for a control panel to open it. However, this door doesn't follow the pattern and the way to open it is by simple moving out the objects that are blocking it. The challenge is nonsense as the objects aren't preventing the door from opening in the first place. No jammed gears or anything.

To lack coherence and cohesion leads  to player's confusion because there is no pattern to follow. It's nonsense.

This is the best puzzle of the game, nonetheless the player has to guess what the goal is. The cube has a translucent track and some targets that shift gravity around when the player shoots at them. For starters the targets don't follow the same design as the gravity devices that shift gravity in other places of the game. This breaks the game's coherence. The player also has to guess that the track is a track and that there is a moving part. Once the player understands that the moving part has to complete the track to connect the energy from one end to the other the cube dissassembles itself and frees the player.

Rubik's Cube is one of the most famous puzzles in the world. In it the player has to twist and turn until all faces have one color only. If the player doesn't know what the goal of the rubik's cube is, they are left twisting and turning it with no direction. This is exactly what happens in prey's puzzle box. Rubik's Cube is more intuitive because with six faces and six colors is much easier to grasp the goal of matching one color per cube's face.

In prey the cube is placed with absolutely no care about giving context or making the puzzle part of the alien's story. Every obstacle and challenge throughout the game lacks explanation or context.

In here there is a platform up there and two control panels. Activating one panel turns the energy on for a few seconds and then it turns off. What do you do? The developers were expecting the player to guess that the trick in this puzzle is about time. Does the player have the power of super speed like the flash? No. The power that the player has is to spirit walk and this allows the player to leave the body in a specific place while the spirit activates something from far away. That's the trick to solve this puzzle.

The puzzle is not well made. Nothing in the environment gives any clue about the behaviour of the control panels. What the player notices is that the cables glow for a short while and then immediately turns off. This behaviour gives the idea that there is either a short circuit or something needs to be repaired for the platform to work. It doesn't direct the player to think that the player has to be standing in two places at once to activate the platform. Once the player does, lights remain on, which doesn't make any sense compared to the behaviour of each control panel on its own.

All shuttles in the game could fly in all directions. The last one is an exception to the rule. The tractor beam mechanic is replaced by moving towards the planetoid while the shuttle can't fly freely, it can only turn up / down / strafe left / right.

What the goal is? This shuttle has an electroshock weapon that requires the player to get close to the planetoid to use. The player has to get close to the red lights and use the electroshock weapon to activate it, which turns on an energy beam. The devices that are off, not having an energy beam being fired, have the same design as some security turrets that would  fire at the player in other parts of the game. The developers were expecting the player to guess that they have to use the only weapon at hand on those devices on the planetoid. If the player's shuttle hits an energy beam it's temporarily disabled, which is a rather counter-intuitive behaviour. It'd had been more logical to destroy the already on devices on the planetoid. After turning on all beams the planetoid explodes. The explosion itself being another illogical behaviour.

Does the planetoid represent something? In other parts of the game the player has interacted with planetoids but they never have a purpose in the alien's mega structure. The game never explains anything.

After solving the planetoid puzzle the final boss in inside a huge football. The football is invulnerable. What now? If the player looks closely the hexagons have a marking indicating that they have to use the spirit walk power. However, the game never explains or gives any hint, the player has to guess that the panels must be shoot with spirit arrows, which turns them white. Then what? Again, the player has no clues and intuition tells that the player has to shoot all panels, turning all them white. The player is going to fail to do so because there isn't enough time to do that before a panel turns back to normal. What the player has to do is to shoot with an spiritual arrow and then again with any regular weapon. The game never explains how the aliens are vunerable to spirit arrows anywhere. The challenge is completely out of context and lacks any coherence.

After the last puzzle of the game the player is transported to a strange place that resembles an alien dimension. It seems to be a gas planet. The boss is protected by an indestructible shield. What to do to kill it? There is a nearby control panel that launches a device in the air. The player has to guess that the device is in fact a bomb and shooting at it detonates it. In spite of the explosion radius the bomb has to be detonated very close to the boss for it to disable the boss's shield for a few seconds. The last challenge lacks any coherence because if the boss is protected by an invulnerable shield, what does the bomb do to disable it? It's a regular blast with nothing special about it.

Image credits: Gamer Max Channel

The first sealed door in chapter 3 is counter-intuitive. When the player goes downstairs in the dark room they find an inactive seal with a protective bubble. After going to the courtyard and fighting all the demons the player finds a sealed door. Going back to the dark room and the seal is now active and ready to be destroyed. Why does the seal activation trigger after the player fights the demons? It's like asking to turn on the lights by turning off the power.

This only happens if the player goes downstairs first. But the level design ends up directing the player downstairs rather than to the courtyard first.

Detention Center mission. In one of the detention center's floors there is a forcefield that needs to be deactivated for the player to pass. The problem is that the switch that turns it off is located in a dark corner and far away. The switch turns off the forcefield for a limited amount of time. If the player doesn't run back to the forcefield he or she is left wondering "What does that switch do and how do I turn off this forcefield?". In another floor there is another forcefield that keeps blinking. This time around the player shouldn't have a hard time figuring it though, because just by staring at it the player should notice that there is a certain interval when the forcefield turns off and thus, allows the player to pass. 

It can be argued that whoever designed the level had puzzles in mind. The problem is that there are no clues and the player has to guess by trial and error.

In Duke Dome there is this puzzle to pass. The player can clearly see where they should go because there is no other way. The clues left for the player are pretty much an exercise of guessing what they wanted the player to do.  The player has to follow the lights because they signal where the player should be looking at. The rest is about guessing. The red barrels explode and shooting at the red barrels inside the container makes the container tilt. That's a hint on how to pass this area. 

The problem with this sort of puzzle is how it's completely disconnected from the game's mechanics and even intuition. In real life people would naturally use a barrel or a box to step on and get higher. When the player is inside the tilted container he or she is very close to the edge and could naturally jump to get there. Yes, the player can jump but there is no grabbing onto ledges in this game and the player won't be able to jump from inside the tilted container to reach there. A light inside the container and two tied barrels can mean anything from nothing important to anything else that is unrelated to what the player has to do to progress.

In previous areas there were other containers and pipes that would fall to let the player use it as a bridge to reach their destination and the developers were probably expecting the player to just see through that pattern. I'd say that even something small such as adding a line of dialogue can help here because what is obvious to the developers may not be for the players, specially if the developers or designers are bad at conveying or communicating their message or intentions.