While trying to do the Kidnapped mission on the USS Kirk, I would beam in (without my away team naturally). After a few seconds they would show up but then I turned into a ship, but I was still my toon. Meaning, I could fly, roll, and had the ship action bar, but couldn't fire phasers or torps. I was however amazingly resilient, even used the Klingons' own plasma fires to kill them.
I've beamed out and in several times... I might have finally gotten lucky enough to where I can actually play this mission now. *crosses fingers*