Abandon Shipping: In the anime, Arashi/Miwako was quite popular, until it was revealed that he raped her out of insecurity. He was redeemed for some in the manga when it was shown that he feels horribly guilty about the rape and is constantly afraid that she will leave him for someone "better" (ie. Hiro). It's clear that after Hiro sets him straight about her feelings for him and he realizes that she loves him for who he is, he becomes more confident and his attitude improves. (In fact, he and Miwako end up marrying and having a baby.) Not that you'd know this if you've only seen the anime.
Viewer Gender Confusion: In the manga, Yukari questions Isabella's "biological sex" pretty soon (she's dressed as a woman, but is absurdly tall and completely flat-chested). In the anime, they favored a more ambiguous (or should we say, direct) approach, giving Isabella a female voice actor.