It's not just a couple of comments, it's been going on for years. She published a huge rant about trans people on her website. She has taken part in numerous events run by anti-trans campaign groups, and has repeatedly endorsed others, in some cases confirming that she has given money to them. She accidentally copied and pasted some text from an extreme anti-trans blog post (that she had presumably been reading) into the middle of a tweet aimed at a child. She then lied about this situation and claimed that trans people were angry at her just because she praised a child's drawing. She gets incredibly defensive and angry at anyone who disagrees with her. For example, Graham Norton was asked about her, and he very politely said that he thought the media should talk to trans people and medical experts instead of celebrities - she responded by accusing him of supporting rape threats and death threats (this is a common theme - she has received some rape threats and death threats, and therefore anyone who disagrees with her is essentially a rapist murderer).

On top of all of that, people have pointed to several questionable depictions of trans people (or characters who seem like they might be trans) in her novels. In one of her detective novels, the hero threatens to get a trans woman locked up in a men's prison, where he suggests that she will probably be raped. Some of the others are more of a stretch - there is a minor villain in Harry Potter who is a woman who seems to have very masculine traits. Some people think that one is a coincidence, but some people think the character lines up perfectly with how she views trans people.