Started hitting more of these so I figured I'd make a thread and just update it with what I found.
So far a few times upon completing a check the "next" arrow will just dissapear and I can't progress. Closing the game and reopening it seems to fix this (I'll try to get better repro steps)
Blackfang Dungeon
Shrine of Lamashtu
Cast Detect Magic
Encounter Blessing of Shelyn
Expanded Spellbook fires on Ezren
Never take damage from Shrine for encountering a blessing
More as I find!