There's several bugs with the Auto-Pause mechanics. I'm going to try to list what I see here (and maybe some suggestions); anyone else please chime in if they notice anything else.
Weapon Ineffective triggers on buffs, status-inflicting spells, etc. anything that doesn't deal damage: self-explanatory here, seems like the game is interpreting something like 0 damage and triggers the pause. Can Weapon Ineffective only trigger once and stop repeating on every strike on the same enemy? There are times where there's nothing I can do about ineffective weapons (because there is no appropriate alternate weapon) but I want to keep the party member (or summons, pets, shapeshifts) there to tank hits. Likewise for Extraordinary Defence - see #2.
Spell Cast triggers pause on all abilities - including friendly: says in the tooltip that it only triggers on enemies. I personally would only want it to trigger on abilities from enemies, there's already another pause feature for party ability triggers Just nitpicking here, but it's a bit annoying when Character Death/Low Endurance triggers on the cheap summons my Chanter brings out. Not sure if it needs to pause when they're occasionally 2/3HKO - almost all at once; I get a lot of spam there.