What the title says is what's happening. I'm not sure if this bug has been present in previous versions of the game, but it happens in the current one (0.7.1), so I thought you needed to know.

The elevator is seen from SCP-106's chamber. The player is stuck in the elevator when he enters it. The door before the elevator's door intersects with the window, this does not affect gameplay however. (the size of these images has been reduced to 50% since I was playing in a 1920x1080 resolution)

Seeds where this happens (I'll probably add more if I find any):

• ipj02t

I'm guessing this could be easily fixed by moving SCP-106's chamber and the warhead room away from each other, anyway it doesn't make much sense if they built the rooms so close together (imagine if 106 ruined the warheads)

Personally, I think the warhead chamber can be replaced into the third zone instead of the second. I think it would actually make a bit more sense to have it in a clean, well kept part of the site the doctors handle. Looking at it now, it seems VERY dangerous to house a 5 megaton hydrogen bomb in the area where the most dangerous and unpredictable SCPs are located. Plus, I feel that the sterile environment of the office zone suits a detonation room more.

Placing it in the third zone would probably fix the bugs shown here.

BluePhoenix wrote:There are also intersecting map pieces in 096's room.

Spoiler

I was only able to take this one picture.

Do you still have that save? Maybe you could tell us the seed where that happens.