I had a very similar issue with Chants of Sennaar (another incredible game), where there were exactly 3 words I was missing, I knew what they were, but couldn't find them. I kept going anyway and found one (by a different method than usual), then eventually after scouring the whole map twice had to look it up and there was just a stairs down the edge of one section that I didn't see at all, but which also didn't respond to the "hint" button that normally shows you any direction you can go or thing you can interact with.

Also very glad I looked up the solution for the Obelisk puzzle in Fez as there was no way I was getting that (seemingly incredibly contrived, but apparently not correctly solved yet) solution.