>>282364195
Its complicated and people will give different reasons, sometimes people can't articulate what is actually bothering them about her and fallback to some obvious but not that revealing aspect. People will instinctually say Mary Sue without really knowing what that means or how it works for why it bothers them, so lets go with some basic ones.
There are at least some people that are in for waifu wars and so Emilia offends them for being either competition or "beating" the girl they think should win. These are usually anime-only casuals and they're not that active though they're probably numerous if you forced every person who watched the series to chime in.
Second are people who think Emilia is boring. They don't hate her per se, though this apathy might become hate if they're forced to sit through too many scenes with her that they view as utterly irrelevant and wastes of time. This happened to a number of people in S2. Most of Emilia's scenes didn't add anything, but she was crowbarred in while more interesting things were cut to make room for it because she's the designated main heroine so she deserves all the screentime. This causes resentment that can transform into actual dislike.
Third is similar to the above. She's supposed to be important but frequently doesn't feel like it, yet the story and marketing and all that shoves her down people's throats regardless. Some of this can also be from people who felt lied to, i.e. they liked her in Arc 1 and then that character they liked seemed to vanish and some dumb bimbo replaced her and they're hurt and confused.