What Should I Do?

Yes, you should.

The stuff that was on the coin does not magically disappear. It is now dissolved into the acetone. As that acetone evaporates, the concentration of that gunk increases and at some point starts to redeposit on whatever remains, whether it is the bottom of the container or a coin.

Definite good advice. Now I DO cover the acetone while it is doing its job so evaporation is minimal, and I don't let it get low enough that I was able to detect residue, but new advice heeded form now on.

I used to clean literally hundreds of glass insulators in three gallons of concentrated HCL. One batch of acid was used for close to 1000 pieces cleaned. It would stillbe my cleaning batch, but I did not want to transport the acid when we moved. The soot on the glass settled to the bottom, but the HCL still made crystal clear glass - and it took about 10 seconds to do so. So I guess without thinking too much about it I was making a parallel with coins and acetone.

Another mistake I now see I made without thinking about it is that glass won't corrode like coins, so the situation is very different.