[Q]

I recently had a game were I surrendered several smaller empires to a AI-empire to create a huge mega-AI empire (makes a really challenging opponent). Again the surrendered ships and planets were not under a minister control. However I did not wait long but corrected it manually as soon as I realised it: if you switch the AI off and immediately on again all planets and ships are under minister control. So IMO this is a bug and it should be not to difficult to correct it. Mail it to MM if you didn't do that already.