Is this the closest to a bug forum we've got?
Anyway, when you cast domination on a unit, it retains its original fleet assignment (AI apparently puts everything in fleets and I haven't tried the ability on another player yet) and orders, which is extremely annoying. If you dominate a unit that's fleeing, it'll usually flee with the rest of your opponent's army and then get quickly smashed on the other end of the phase lane. This is more of a problem when you have the ability on autocast and aren't paying enough attention to micromanage them, but even if you do, it's annoying to have to press leave fleet on every ship you dominate.