I had the same problem. I couldn't find one last golden skulltula and I had golden skulltulas all over the hyrule map. The solution is simple. The hyrule map doesn't tell you if you have all skulltulas in a dungeon or temple. So, go to every dungeon, temple, and even the well and then look at your map. Does it have the GS symbol? If so, then move on to the next temple/dungeon or well.
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Topic: OoT HELP!
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