What causes this?

I don't know about cleaning, but at one time coin doctors were using laser to spot soften/melt gold coins to remove contact marks and light scratches.

 

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@Conder101 beat me to it so I'll just confirm that doctoring coins using a laser is still being done. many coins were slabbed before the two top TPGS's caught on to this type of alteration. Most I have see are repairs to the fields of high grade P/L gold.