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I just finished the game and I believe I collected all upgrades and collectables but when I look into the menu where all my items and abilities are listed it looks to me like I am still missing some as there are two spots that look like there should be some items placed?

In other words are there items that are not necessary to get to complete the game that I am missing? I'm not talking about the Power Seals but object that go directly in the Items category in the menu.
It's intentionally like that, you have all of the items. Though with the Version 1.0.4 update, the Power Thistle remains in your inventory rather than disappearing after feeding it to the ogres. With that update, there's only one empty slot now.