Clients are receiving late filing penalties on those extensions. The problem stems from the fact the IRS was not processing anything sent via mail i.e. extensions, POAs, tax returns, correspondence, etc. It is my understanding they are beginning to process things now. A letter with proof of filing the extension may resolve the penalty issue but be patient.
IRS has a First-Time Penalty Abatement Waiver policy that may also be used if all the criteria are met. It applies to individual income tax returns and to certain business returns, including partnership tax returns.
[Internal Revenue Manual Section 188.8.131.52.3.2.1]