A pretty large bug with the "Depose Antipope" Casus Belli is when a future vassal is independent or rebelling and creates an Antipope, then after being incorporated into the larger kingdom/empire the only way to Depose the Antipope is by internal vassal warfare. The vassals liege can not remove the Antipope and external entities can not force its removal.
In my current game with the latest beta version there are now 2 Antipopes by separate dukes within the HRE (appointed during rebellions) with no way for me to remove as an external power, even when they die they continue to have successors hurting Catholic Moral Authority.