Not that any of them were that hard, but Lakebed Temple did confuse me somewhat trying to redirect the water flow. Also the second room with all the spinning cogs, the one with loads of clawshot targets, gave me trouble trying to get all the chests. The only other problem I can think of is when I missed two of the Poe spirits in Arbiter's Grounds and had to backtrack for them.

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Thanks to Kynnella for the sig.