What could cause a matching divot on a CPU and cooler?

A matching mark could be from something trapped between the CPU and cooler, or from a surface defect. The description alone is not enough to tell whether it is damage or residue. Don’t scrape at the CPU with anything abrasive. Clean both surfaces gently with isopropyl alcohol and a soft, lint-free material, then inspect them closely.

If the marks are genuinely indented into both surfaces, I’d avoid assuming they are harmless. A raised burr or loose fragment on one side could have made a corresponding mark on the other. Check for anything loose or sharp, and don’t mount it on a replacement CPU until the cooler’s contact plate is clean and smooth. If you’re unsure, replacing the cooler is the low-risk option.

Clumped paste can make a spot look much worse than it is. Try a careful clean with isopropyl alcohol and look at the surfaces under bright light from different angles. If the CPU still works and there’s no obvious cracking, corrosion, or loose material, the mark by itself doesn’t prove the cooler is unsafe. Keep an eye on temperatures after reassembly.

There are reports of dark marks appearing on both a processor and heatsink, but the cause can’t be established from appearance alone. Unusual paste, contamination, or surface damage are all possibilities. I wouldn’t use a knife or abrasive pad to test it. If the cooler has a deep pit or a sharp edge, replace it rather than risking poor contact.