If it's showing as mappable then it can't be wrong. That said, there are a number of little bits here and there that are require super precise positioning. You don't need to get every single bit to max the title (there's 1031 points across all activities and you only need 1000 - you can skip entire dungeons and still have some carto leeway) so don't stress the stubborn bits. You can always come back later if you really need to.
Regarding that bit itself, I can't really help. You'd just have to keep going up and down really slowly and on multiple angles to try and get right into some nook you couldn't before. Don't stress it.