just to pint out some things that haven't be said already:
1) It has ALWAYS been the case that if you abandon a planet with ships, you loose them.
2) It also used to be the case you didn't have to confirm abandoning a planet that was changed by BFG at the players request you now have to confirm abandoning anything.
3) It also used to be the case you could abandon planets with fleets in motion, again that was changed by BFG at the players request.
So, sure sorry you lost some ships, but thats not down to BFG, thats down to you...your mistake for not checking first