I have experienced the same thing with my Delta Shuttle and the pilot and its passenger was trapped outside it after they unloaded and tried to re-enter. I sent a Bug report to the anti-bugger guys/girls and hopefully it will be resolved soon (Tm) but I may have not sent it to the Asims directly, should I file a second Bug-report directly directed to the Asims or are they flexible enough to find it on their own?
I never done this before? The same ship my poor Pilot is using swallowed five NPCs that went up in thin air and that was never resolved. My shuttle may be hunted or something.
Ps: I thought my pilot had grown to fat to enter. *snickers*