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The brake pads rest on them, there should be clearance, although it is minimal. Do you have any aftermarket parts or using rear base calipers on an S? (which may work for all I know but I thought I read something)
Is your rotor loose for any reason, like you are disassembling? Maybe it is wobbling and when you get the wheel bolts on it will hold it. A totally trashed wheel bearing may allow enough run out to where it might contact the pins as well.
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