Can miss two skill points permanently with the Trial of the Ancestors

Simple to replicate - complete the Trial of the Ancestors quest, but don't speak to Hinekora (just Navali), then close the game fully (so your instance closes).

You can then go back to the room but Hinekora will no longer speak to you. Navali will still give the speech saying Hinekora has a gift, but you receive nothing. The icon remains on the map and lit up to make it clear the quest is unfinished and the points missing.