"I'm sorry you feel this way" is not an apology. It puts the blame on the person who was hurt by the action. Unless you wrote this manga, there is nothing for you to apologize for.
I'm going to assume that you have no idea what transmisogyny is. It is one word that describes the sort of discrimination used against trans women. It's deadly and leads to the sexual assaults and deaths of countless trans women around the world. Trans women are demonized and fetishized simultaneously. They are treated as sexual predators, manipulators, deviants, perverts amongst a host of other things. Thing manga contributes to the falsehood that trans women are forcing themselves on others. The way that her trans identity is revealed is so disgusting and objectifying. She embodies everything that cis people try to make trans women out to be and it is beyond aggravating to see.
I am trans myself and barely see any representation in manga of trans people. It's the same with all media in every country. We're virtually invisible made to feel like we don't exist. When we do see ourselves it's as caricatures of ourselves.
The only good thing the mangaka did was not have anyone misgender her, but I've only seen this translation of it. I have no idea what the original text says.
If you are genuinely confused as to how Mei's depiction is transmisogynistic then I suggest that you follow trans women online, read works by trans women and watch trans women on platforms like YouTube. Watch Disclosure on Netflix if you have it and any other informative work that is done about trans representation in the media. Educating yourself is the best thing that you can do.
I'm tired of seeing trans people being treated as predators. You rarely see them being represented at all, but when you do you get shit like this. I would have been in love with the story had Mei not been included in it. The mangaka is way out of pocket for this. This is so transmisogynistic. Virtually nothing else was wrong with the manga. It could have been a really cute story. Don't do this shit and expect trans people to not get upset!!