every case I've read about has received the standard automatic rejection letter for not filling in the form correctly (e.g. for not including your passport)

given the Home Office never expected EU migrants to apply for permanent residency, the response was appropriate prior to the referendum result

it no longer is, and the Home Office now have updated guidance on the matter

I'm sure it wasn't nice to receive that letter, but it just a case of the government bureaucratic machine responding at glacial speed to change, as normal