but you get better resources lol.

It may have to do with how quests often have a village or workshop that counts as part of your territory until you remove it.  Maybe this happened and the game got confused.  (Just a theory.)

Best regards,
Steven.

I think it was caused by neighboring city growing to level 4 and claiming land between my two cities.  I increased prestige to reclaim the land and that's when it started happening.  I checked my saved games, but the borders look okay.  I will send a game if it happens again.