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
For example, last time I looked at the UK papers they were full of cases of EU citizens, who should have indefinite leave to reside in the UK, being harrassed by the Home Office and threatened with deportation.