If I had to take a guess, it's the "born in the wrong body" narrative that rubbed Andraoise the wrong way (and tbh it annoyed me a bit too), but considering the game's setting, I ultimately didn't mind that much. (Obviously YMMV)
For those unaware, the "born in the wrong body" narrative is an essentialist way of describing trans people. It assumes that there is a rigid male/female sex and gender binary (which excludes/disregards intersex and nonbinary people respectively), and that trans people must have always expressed the desire to be the "other" gender and behave according to the norms of their gender identity.
eg. (According to this narrative) A trans woman is just "a girl in a boy's body": she always insisted she was a girl when she was young, she experiences physical dysphoria over her body and will transition in all the ways that are available to her to correct this, and once transitioned, she will completely conform to female gender roles.
There are absolutely some trans people who describe themselves this way, but it's generally associated with an older understanding of sex and gender (which is why it bothers me less in this specific context: Marie is from the 1920s, where that kind of understanding of trans people was more common).
I don't know if the creator(s) of Marie or this game are cis or trans, but generally it's frowned upon for a cis person to invoke the "born in a wrong body" narrative for trans characters because it's a very oversimplified way of describing the trans experience.