Fighting against human nature is a losing battle
Mark uses the mechanic "suspend" as an example. With "suspend" the players can trade turns and time for mana, paying less mana to cast the same spell. The basic idea is that time is money. Turns being time and mana being money. Some creatures were made with the mechanic. The problem? In magic there is a rule that prevents creatures from attacking in the same turn they come in, unless they have an ability or are granted the ability to skip that rule. During playtest a common mistake was to forget about this rule when players cast a creature with "suspend". The reason for this mistake lies in human behavior. Players know the rule, but "suspend" creates a new context in which a creature is effectively cast but delayed for X turns. After waiting for X turns the creature comes in and the rule accounts for the creature coming in while not counting the X turns that the player has waited while the creature was in a sort of "stand by" mode. All sorts of tricks were attempted to remind the players that the creature couldn't attack even after waiting for X turns due to "suspend". In the end the solution was to give those creatures the ability to attack in the same turn they come in.
Another example is opening a door. In a game focused on exploration such as "The Last of Us" there are a lot of doors. Notice that many doors in the game are already open. Why? On the technical side there are many problems to solve to make doors open and close while obeying to all possible cases that would prevent a door from opening or closing. Most of the problems are related to the enemy's A.I. All those conditions are really hard to deal with. The doors have to look and behave realistically and that's not an easy task to accomplish. In many cases it's easier to just leave the door open than having to make it an interactive object. What about closed doors? If there is nothing but void behind the door the player doesn't know that there is nothing behind the door, unless they open it. To make it clear for the player that the door won't open the solution is to place a visible lock on it. In Shadow Warrior doors that are interactive have a yellow highlight to make that door stand out from the rest. The point is, when a player sees a closed door it's only natural for them to try to open it.
Now I can't go in much details about gameplay experience because I lack the professional experience. I'd imagine that there are multiple factors that have be taken into account before deciding whether a door should begin opened or closed. Atmosphere, surprise, pacing, scary moments, etc. In Rage for example there are doors with interactive locks. The player knows from the game that those locked doors mean that there are goodies inside. In the case of "The Last of Us" the player knows that the locks are non interactive, meaning that there is nothing behind them.
A similar case is stairs. In a game such as Tomb Raider the character has the ability to climb walls and grab on ledges. If the player is in a place where the goal is in a high place and there are cabinets and shelves for example. The player is naturally going to attempt to climb the cabinets and furniture to go up. It's going to be confusing to the player if they can't climb the existing furniture and even worse if the furniture is placed close to the goal. When the player sees stairs the natural reaction is to think that there is something that requires the stair to be reached. However, sometimes the stair is a purely decorative object with no real function. Terrain with tracks have the same effect. They naturally draw the player's attention to think that the track is there to be followed. The track might be a modelling or texturing mistake. The opposite can also happen, with players stepping on places that they weren't supposed to go and gaining some unwanted advantage. What could have happened is that the environment is inadvertently drawing the player's attention in some way that wasn't predicted.
There are small details that can fool and they aren't always intentional. It may be the case of a level design that doesn't match the game's mechanics for example. Games simplify physics and bullets aren't simulated with real physics most of the time. Most games rely on straight lines and instant hit, disregarding bullet's mass, gravity, friction and velocity. A level designed for firearms must be made with those facts in mind and allow players to be hit from a certain distance. On the other hand, if the player has a knife, the level design must account for close encounters. What if the player can throw the knife? The level design must be made with this mechanic in mind.
There is a lot of research about cognition and intuition and much of it can be applied to level design. To limit this page's goals I'm not going deeper into that. The discussion could go on to other areas such as driving on the right vs driving on the left side. Or even how the order of "yes" and "no" impacts on answering questions.
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