i did some testing by spying within the first 5-10 turns on the AI (foreign relation, stats tab) to find out about what abilities they tend to choose and whatnot. i made a shocking discovery.
when everything is default (fresh install, no civ has been edited) and you start the game the AI will pick random abilities. so far so good.
if you then restart the game as another civ and make the AI the civ you have been playing earlier (with ability points spend of course) they allocate another set of ability points adding up with the ones you chose effectively giving them double the ability points.
this seems like a bug to me. if you edit the AI it should have the bonuses you set up and not an extra random pile of bonuses they couldnt have possibly gained through anomalies.