This also happens if you switch characters while onboard
note: It would seem in my experience with this it doesn't just ignore the orders it freezes the ship because i have had this happen and cant pilot the craft manually.
These are some things that sometimes work to fix the crew/ship:
Telling all crew to come to you then return to stations
logging out of game and back into the character on the ship
recalling to the ship while already onboard
switching characters a few times sometimes also get the ship unstuck.
note: It would seem in my experience with this it doesn't just ignore the orders it freezes the ship because i have had this happen and cant pilot the craft manually.
These are some things that sometimes work to fix the crew/ship:
Telling all crew to come to you then return to stations
logging out of game and back into the character on the ship
recalling to the ship while already onboard
switching characters a few times sometimes also get the ship unstuck.