IRS refunded the penalty I owed

In 2023, due to savings interest, when I filed my 2023 taxes, I owed a small penalty (about $40) because not enough was withheld from my paycheck. This was calculated using reputable tax software.

The IRS just sent me a check for the amount of the penalty I paid. If the IRS made a mistake, could this make things difficult for me later? I haven’t cashed the check yet.

I wouldn’t think so. There are a lot of safe harbors for the penalty, and it’s not inconceivable that your tax software got it wrong.