There is a late penalties and interest worksheet in ProSeries.  Personally, I just let the IRS calculate the penalty.

There is no blanket waiver, but if this is the first time they have filed late and they are current on all filings and taxes, you can ask for abatement under the first time penalty abatement provisions

https://www.irs.gov/businesses/small-businesses-self-employed/penalty-relief-due-to-first-time-penal...