Oops, never mind, I went back and checked for all those things you guys suggested and found that the ship did mutiny after all - it's just that when I clicked "goto" to see where the ship was, it went to a different ship, the Alpha Mk3 002
1!
Which was in a nebula... So either the two ships were together and the game tried to go to the Last known location of the lost ship, or since the ship was no longer under my control, the game picked a ship that was adjacent in the ship list...
(great, so now those pesky (empire name removed) have an INVISIBLE colony ship flying around in my territory
)