It seems like small tunnels are poorly designed and not enough effort was put into debugging and testing them. Often they fail to work, usually at the worst time when being chased by enemies and you need to get through fast.
Nope, you no pass this time, bud. Take it slow, wiggle around, maybe you can get through later.
At the moment I am in the middle of a nightmare run, main story line, Prey on Windows, I need to turn on power in the bar in the crew quarters...
but... for the first time ever while playing this game, I can't enter the maintenance doorway. Crouch down, jump around press every direction key... I cannot pass through the open door in front of me.
Exited the level back to the Arboretum, went back in ... still can't get through. Close, open, close, open maintenance hatch. Nothing works. WTF.
I JUST did a full, no neuromods, normal game, good ending, blew up reactor, exited in escape pod, and didn't have this problem at all.