Did you complete the sibling rivalry quest, in the hidden cave on Sentinel Island? That should have removed both the Fake Red Ore and Wolfsbane Poison from your inventory (even if you took the solution that used neither). There is no use for them except for that quest (and no use for Penelope's Amulet, other than to wear or place in the corresponding gravestone).
Before acquiring the battle tower, jump into the water to either side of the (initially) windy peninsula, and you can swim to the entrance of the hidden cave.
There isn't any way to manually get rid of unnecessary quest items. I don't recall, but entering the Hall of Echoes may remove some quest items you can no longer use, but then that is a little late for cleaning up your quest item inventory section, as you will have completed everything else before proceeding there.
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