Does anyone know where the last gathering location is here? I can't seem to find it for the life of me. Every time I finish the map I don't get bonus 3.

Here's a screenshot of my map:

Near your Sharty.
Equip her with Adventurer.
Its a place where you can mine for collection.

Ah, so I can't get it on the first run there. That explains it, walking into that room triggers a cutscene so I couldn't look in there.