945 Filing

Apparently, the withholding tax on a distribution made in 2021 was paid in July 2022.

How would Form 945 be filed, on a 2021 Form 945 showing amount due?

How would IRS know the tax was paid and when paid, or is it up to the client when IRS sends a notice.

I don't know if there is a penalty for late filing.

When payments are made through EFTPS you must indicate the form (945) and the tax year (you would indicate 2021) even though paid in 2022.)  The IRS matches the 945  with payments in their EFTPS system.  The IRS would apply the early 2022 deposit to the 2021 945 assuming the electronic payment was marked 2021 in EFTPS.  Yes there is a penalty for late deposit.  But deposit deadline varies - most of our plans are the 15th of the following month but some have a semi-weekly (not bi-weekly) deadline.