PAYE50915 | Employer returns: employer starter and leaver forms: employer e-file in-year penalties: manual issue of a penalty
From HM Revenue & Customs · PAYE Manual
The manual issue of an in-year penalty can only be done using the E-File In-Year Exceptions List screen (PAYE50955). The [Issue] button allows you to manually issue a penalty. When you do this ECS will automatically display details of the penalty to be issued in the E-File In-Year Penalties screen.
You will not be able to issue a penalty in the following circumstances
The E-File Permanent Inhibition signal is set
The Insolvent signal has been set
The scheme type is exempt
The RLS signal is set
The E-File Temporary Inhibition signal is set