Yes, the other two positions in the engine compartments are actually there, they just have a graphic used to mark them as inactive and they aren't counted. So anytime sailors are moved "automatically" into the engine room, as in when you submerge and the Electrics take over, or when you rclick Man Room or whatever it's called, it'll end up "overfilling" the room. Other than the annoying picture, it doesn't really hurt anything.
