This sounds similar to an event that happened to me the other day when trying to leave the Ebon Hawk on Dantooine after the Visas encounter, turned out the save file got corrupted somehow.
Other people on the board have said that this is a very rare glitch that you may not even experience in several plays.
Try restoring an earlier save and replaying the area and see what happens, I restored a save before entering the Ebon Hawk, replayed the fight and that cleared it up.