The problem is that the anime are showing stereotypes and suggesting that transgender characters can’t be taken seriously.
This kind of caricature is almost exclusively used for transgender characters who are harmless but only have value as “joke characters.” The transgender women in Gintama are examples of this. In general, they are shown with “comically” over-the-top masculine features and large or tall body types.
Transgender women in anime are sometimes called Okamas (which is basically a slur, much like queer used to be until lately). Let’s start with transgender characters who are portrayed rather terribly.