I'm through with 6 zones (Great Plateau, Dueling Peaks, Hateno, Lanaryu, Lake, and Faron) in my "Get Absolutely Everything on the Zelda Dungeon Interactive Map" playthrough. I've justified all discrepancies on my way except for three treasure chests that are on the map that I cannot find for...
True on the seed locations. If you've seen the map that comes with the Official Guide, they use arrow trails for the Korok Seeds that are races and flower trails. It's pretty nice.
Another small one...south of the Lanaryu Tower, in that area with tons of bones, there is one of those big craters that normally you knock a large boulder into to get a Korok. The zeldadungeon map doesn't have a Korok listed for this hole - I was able to check off all the markers in this area...
I've beaten the game once and I am replaying, going for 100% with the (excellent) zeldadungeon Interactive Map. I've finished Great Plateau and Dueling Peaks, but in Hateno, there is a chest on the map, and I can't find it! It's in the village, at the river bend...looks like there's a Purple...