So I am playing Advent Loyalists.  It's late game.  I have all of the techs researched except the pacts.  There is only one race that I have any relations with and it is just trade and cease fire.  Anyway, I noticed that while I was playing the fleet logistics cap would move wildly when I wasn't building ships or had any qeued.  I like to keep 10 fleet point open in case I need to build a starbase somewhere.  What I discovered was that somehow ships were changing ownership to me!  And so I had to find them and scuttle them.  Even a diplomacy vessel switched to mine!!!  And what's worse is that they don't exactly do what I would want them to niether!  In this game, I have chosen NOT to use and ship capabilities that permanently mind control enemy ships, so I don't know what's doing this and it blows!