I would be totally fine if there were any alien freighters etc. but there arent any. They keep getting created without any alien presence. I thought about deleting the main pop on the conquered planet and then to create a colony on it again just for the sake of seeing if it keeps happening or not.
The next time one shows up, save the game and open the database. Then poke around until you can figure out what is there. Is it population? Installations? Minerals?
Worst case scenario you can pop into the DB and delete the offending NPR and all associated entries. Needless to say this is the risky approach so make a backup before you attempt this but an NPR that no longer exists should be unable to make new colonies.
How do I do that?
FCT_Race is the table where the NPR is stored. However, since you are doing a manual deletion, the game won't be doing the usual cleanup that needs to be done. You will have to make sure that tables such as FCT_Ships, FCT_Population(s?) are purged of all entries that are associated with the appropriate raceID. Failure to do so will almost certainly break something in the save - which is why you need to make a backup in case you miss something and cause irreversible damage.
My recommendation is to find the NPR in FCT_Race and turn the NPR from an NPR race to a player race (there should be a binary column "NPR" with value "1", make that "0"). Once you do this, hop on the save, turn on SM and select the NPR race. SM delete everything that you can about that race through the game (document stuff that you can't delete as you need to enter the DB for that) without advancing game time and save the game, this way you've minimized the chance of missing something important. Finally delete the NPR and hopefully, your troubles will stop.
