Code S means the distribution is from a SIMPLE IRA. That is why you are getting that message. If you agree that the money is an early distribution from a SIMPLE IRA, you can just check the IRA box.
If you don't agree, or you aren't sure, contact the payer who issued the 1099-R and ask them why the IRA box is not checked. They can either confirm that the box should be checked or that your code needs to be corrected by them.
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