As I was unsuccessful calling HMRC (5 days in a row call was cut off after more than 1 hour waiting time), hoping to get an answer here.
I have filed my self-assessment for 2021 on-time and as I could not pay full amount, I set up payment plan. I have received two letter confirming payment plan in late March 2022, before 1st of April deadline.
However I have now received a 5% penalty for paying my taxes late.
According to this article this penalty should have been waived: