Specifically, this is what happens: if a move requires two different items to learn, the first item eventually will disappear from the cost, but with an empty space where it was. The move cannot be learned, even if all items for the cost, including the invisible item, are in the player's inventory. The only way to fix it is to delete and re-add the items with the NPC editor. This is an issue for big tutor setup areas with multiple item costs.
As this is something that randomly happens over time, it is difficult to reproduce. This bug also occurred in 1.12 versions, but since it's sporadic and hard to gather info for, I hadn't reported it til now. Since I found it's still an issue I thought I'd at least drop it here even if I don't have a lot of data for it.