There are a few things you can do but everything I know kind of requires mucking about a bit in the database, so just make sure to make a copy of it before doing anything. Anyone please correct me if I'm wrong or if there is a better way to do it.
First if you don't have it get something like SQLite.
One thing you can do is just to manually look inside the Gamelog (table FCT_Gamelog) and go through each event to see what is happening each increment and identify the ships involved. This kind of issue can be caused by nprs and spoiler trying to fight but having problems preventing them from doing so, nprs trying to refuel, etc, it's generally only going to involve ships.
After you find whatever the problem is the most secure way to solve the problem is to make whatever alien involved playable (table FCT_Race, change the NPR bit from 1 to 0), then open the game, get into spacemaster mode, change the race you are playing at and do whatever you need to do to the fleet(s) you identified as being a problem. Generally that means deleting them. After that just change back the NPR bit and restart the game.
I had an issue with regular error messages that had something to do involving missing spoiler ships in some fleets I think. To solve the problem I had to remove all of this spoiler's fleets, though you might not have to go to the nuclear option like I did.
