I've noticed this a couple times now. Once I attacked a base and if I tried to enter a door and walk to the square just inside it would see an alien and stop. At this point I just went ahead and threw my stun grenade to hit the commander. After the attack landed, my interface almost completely froze up. I can still move the mouse but I can't click any options.
Just a few minutes ago I was on a UFO crash and did the same thing almost. Went to enter the door, it opened and saw an alien and didn't take the step into the room. I attacked with my plasma rifle and after the attack my interface was frozen up again.
Just to test it, I tried it again with a different unit in the same situation just now. The attack goes through but then nothing. The movement square beyond the door in all cases also had a ? on it.