Unsure if this will be at all helpful to anyone else, but if you have a Wilderness map stuck at 95% completion despite having gotten everything else, you might need to go into the mouse trap room (very clever name i know). In the entrance to the Secret Hideout, enter the wrong code and go into that room. You get a unique h-scene game over if you open the treasure chest, but I think you can just leave (not 100% sure on that) if you want to.
Maybe I was just being stupid or something, but I saw the outline of the (fake) door and had no idea how to open it, since I never input the wrong code. So I was just really confused for a while until I saw my map stuck at 95% and tried that. Something something suffering from success.