Why do some items have the Saints logo next to them?
They're DLC items. Maybe you've got them as a preorder bonus:
If Saints Row: The Third was pre-ordered, this DLC was added for free.
For example:
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Battalion Pants are from Explosive Combat Pack.
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Reality Climax Pants are from Funtime! pack.
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Space Princess Tights are from Warrior pack.
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Witch Pants are from Witches and Wieners pack.
And some of them also include vehicles.