In Duke Dome's level there is this scripted event where the player is lifted and has to shoot at enemies coming in a parking building. First, the dialogue that happens between the two characters is meaningless and takes a lot of time. Second, when the meaningless dialogue ends the player is punished because both characters are killed by an alien. That's almost maddening because most players would expect some reward for waiting so long. Third, the player is lifted up but cannot jump to the building even though he or she is so close to it.

In the "Doctor who cloned me" expansion the same thing happens. There is a NPC stuck in a door asking for help. After traversing a long way with many obstacles and enemies along the journey, the player finally reaches the other side of the door. Upon trying to release the NPC, the door malfunctions and crushes him. The player is again punished after having to overcome so many obstacles.

In Cairn Docks there is a boss fight. The player has to fight two shadow troopers in this arena. The event is not wrong in itself. It's the placement and timing that feels off. In the previous level the player has navigated through environmental hazards, obstacles, traps and then finally reaches this place. After the battle the player has an anti-climatic point, because the next challenge is to go stealth and navigate through even more environmental hazards.

Drastic pacing shifts should be avoided. I can't really know what the developers were thinking and what type of challenges they had during their time.

Chapter 2. When the player reaches this bridge in the level a demon flies to the left. There, a troop of demons is crossing another bridge. It's only natural for the player to follow that direction in the channel. When the player reaches the bridge it's a dead end with nothing though. In the next chapter the same thing happens with an exploding car and fire. Having bright and strong lights on dead ends in something that frequently happens in this game.

The scripted event of a demon flying to the left and demons crossing a bridge may play a role in the plot. But if a game is going to have such events they can't be done like this, guiding the player to the wrong side.

Favela. The player's captain sends a radio message telling the player that the target has gone to the west. While the player hears this message a character jumps over a fence, but the player's path isn't that way. A game should make it clear when a character should be followed or not. 

Bad A.I. is one of the sources of most complains in games. The first mission in Quake 4 is to escort a medic from some position back in the same level. The medic has a weapon to fight for his own but at the same time he can easily die in combat, which results in mission's failure. This isn't an issue with level design per see. It's more of a failure in the programming or scripting department. Players hate when they have to rely on A.I. that fails to do what they want or need the A.I. to do. The most annoying part is that if the A.I. fails the player loses and it wasn't their fault, but the A.I.'s fault. Even worse when the A.I. blocks the player's path.

What I could criticise about the first mission in Quake 4 is that the player has to travel back in the level, which is tedious to do because the player is traversing the same areas twice. To compensate for the repetition the level design did care about some scripted events, which reveal a hidden corridor under the floor and there is also an explosion that blows up some pipes. Apart from that, it's pretty boring to be forced to travel back just to escort a medic. It's an issue related to the pacing of the game.

In chapter 6, an explosion sets the building on fire and Max has to escape it. Right before going upstairs there is a dialogue with Max narrating that he is either going to die crushed by falling debris or burned to death. For some odd reason there is a cutscene, the camera's angle shifts to another perspective but the player is still in control. If the player does nothing and expects the game to move Max on its own, Max dies crushed by falling debris. I have no idea why they did this. When the game shifts to a cutscene the player expects that he or she is going to just sit down and watch whatever the game is going to show. However, in this particular scene we have an interactive cutscene and the player has to walk upstairs manually. I died there multiple times not understanding why couldn't Max go around or do something else. Searching the internet revealed more players confused about why they couldn't get past this scene.