I’ve had something similar with a transport ship; in the “Isis hear my plea” campaign at the end you transport Amanra, and not once but twice when I ejected her she came out where I put her into the ship. In my case I had a large army along with and I think the issue had to do with no good landing spot being available, on the third try I moved some of my units away from my landing zone and then she exited at the proper spot.