Sorry if this is duplicit post, I did check other messages only brifely...

When you conquer planet with some of its buildings infested with spes, there is no way how to remove them. Spies are shown only on planet screen, there one can see that affected buildings provide no bonuses, but in Spy screen, those spies are not listed, so there is no way to nulify them... In my last game they remained on that planet till the end...