Personly I've had the same happen to me often. Mostly when useing the original games in Dosbox
Worst case was a Xarquid? (The big Jellyfish thing), get caught in a 2x2 room with a one tile door on a Alien colliany mission - at least I think it was a colliany mission.
BTY - why do the aliens in TFTD always hide in the 1x1 sized rooms while on the terror missions, do they have a fasination with small spaces or is it just an AI problem?