Here are a few situations where you might seem to be stuck, but it’s actually Working As Intended. I’ve spoiler-tagged the solutions, but the scenarios themselves are slightly spoilery. So, you probably shouldn’t read this unless you’re actually stuck at the moment and/or have already beaten the game. :-)

Situation: I’m in the catacombs. I’ve killed everyone, but can’t get through the locked door.
Hint: You’ll need to manipulate the lights in order to open the door.
Solution: There are three statues in the catacombs, each displaying one of the three primary colors. Touching each statue will turn its color on or off. In the central hallway, you’ll see the resulting color created by the combination of the three settings. You’ll need to create one color for each of the three candles in the following room. Whenever you’ve matched a candle’s color, its barrier will disappear and you’ll be able to snuff it out. Snuffing all three candles will open the door.

Situation: I’m in the nightclub. I keep killing marines, but they won’t stop coming!
Solution: There are an infinite supply of marines. You’ll need to make a controlled retreat up to the top of the club, then meet with Kali and defend your decker to proceed.

Situation: I’m underground, stuck in a small rocky cave, and enemies keep on coming forever! WHY DOES THIS KEEP HAPPENING?!
Solution: You’ll need to shoot the walls down in order to escape. Targeting can be a little wonky, but try clicking near the waypoint to the southwest until you locate the target.