If she mailed a check, she could write 2019 on it, but if she paid it online, it will not allow you to apply it to a passed date. It is too late to make an estimated payment toward 2021 online, as of Jan. 18, so that may be the case even for checks. 

The client needs to check their IRS account and see what happened and they may need to call the IRS to find out if that payment, if recorded, was applied to or can be moved to the correct year at this late date.