I've seen a similar issue; my Cherokee conquered the Powhatan, removing them from the game. Yet, I kept getting messages in the log that my neighbors were improving relations with the Powhatan after their demise. This action does not show on the diplomatic screen, only in the game log, so I'm left to assume that this is a bug, and it severely gimps the AI as their diplomats are presumably tied up, constantly traveling back from an AI that no longer exists.
Before, nations that were out of play were removed entirely from the ledger, but now they're kept for purposes of the score system, I think? That might be why the AIs still treat eliminated tags as if they were alive?