K, this is strange and it could be a FRED/SCP bug...
I made a mission in which a transport should undock from an Arcadia and warp out using the hangarbay of a nearby destroyer. It never undocks. It keeps pulling the poor station with it and ramming the destroyer with it to death.
First I tried using SEXP's to give orders. TRansports starts docked, 2 seconds after mission start it gets and AI order to undock and several seconds after that it gets an order to deprat.
That didn't really work, since the transport judt stood there, not moving at all.
Then I tried giving it initial orders to undock (89) and warp out (60) and the station-pulling happened.
It's fin, but ti's also frustrating.
Oh, using other head ani's doesn't seem to work either. I extracted a few from Blue Planet and used them for conversations - the stock ones appear in-game but the new ones don't.