I noticed some strage AI "political" behavior at times as well. For instance, you encroach some tribe's land, they are ok with it (they don't declare war) and suddenly some other indian tribe becomes furious that you 've stolen their land.
I noticed this kind of strange behavior a couple of times that I regenerated the map and then played the new one. So, I made an hypothesis that if you regenerate map somehow the system mixes the old with the new ownerships of land and it becomes a chaos. So, after that, I just don't regenerate map any more, a few more clicks to start a new game is not so bad in comparison to the time you invest to play a game.
So anyway, if you have regenerated the map and played on the new one, maybe this could be the case, mixed AI ownerships (confussion) and capturing those cities triggered many tribes to be angry at you. I'd be interested to hear if you did so.
On the other hand, I also noticed some times multiple ownership over some tiles from different indian tribes that were neighboring and I consider it "legit" (ok). So you can check this out too.
Regards,