[Q]

Lucas, I think if you just remove all espionage projects (with the only exception may be of technological espionage) it will be fine.
Alpha Kodiak, I had a similar experience. Did you notice if the individual minister was switched on for this ship? But anyway I think this is a small bug. However it is still very annoying, if a vital ship like my population transport with citizens of an another species (I don't like the word slaves) is the target of a crew insurrection. It took me quite a time and effort till I captured it back. So I think the AI should continue to use it.