Edited to add: this was supposed to be a quote reply to @RosesAndHellebores
I took the article's description of the events to mean that she referred to the patient as "a mister", not "Mr X" i.e. a commonly heard colloquial way of saying "a man".
"In the eyes of Epsom and St Helier University Hospitals Trust, the greater sin was that Ms Melle had referred to Patient X – who was born male but now identifies as a woman – as ‘mister’ and ‘he’ during a phone call with a doctor. It was this which prompted Patient X’s aggressive outburst."
However, it's ambiguous and I fully accept that's supposition on my part. If the nurse had said "Mr X", ideally the article would have written it like that.
Either way, the nurse didn't say anything wrong because she was talking about a male patient's clinical care. We have no reason to believe that this particular nurse speaks about women any differently, either colloquially or as Mrs/Miss/Ms X.
It sounds like your concern about the hospital's treatment of women in general is a related side issue to this case. The main issue here is how the nurse has been abused by a patient and then treated in a way that is unlikely to be lawful by the NHS.