I had another game where the last Muton would not leave the hangar.
Easily 60 turns passed after killing all the othey guys. It was a navigator who had panicked. Occasionaly he would make a hangar door open and close. I had at least 26 men left (maybe 28 or 29), max eqiupped. All entrances had prox grenades.
At first, I hoped he would bleed to death (had that mod and the aliens don't expose themselves mod).
For the 1st 30 tuirns, I hade 1 guy facing every entrance he could use.
I pulled them hoping he would charge. No such luck.
After 60+ turns, I sent 2 guys into the lower right \ hangar (had to grenade my own prox), searched, found no aliens and 3 blaster bombs. I fire 2 blaster bombs. I use 1 to clear out the 2nd floor of the room before the Lower left hangar. That took out both of my prox in the area. I send a second to punch a hole in the hangar door. Immediately sent 2 guys, who found the lone baddie in a turn. Killed him. Victory.
Aside from a bug, I wonder if he had any weapons. Maybe he dropped them and were destroyed at some piont.