That's sort of like asking in what way are African-Americans treated differently under US law. Sure, the law may appear to be equal for all legal members of society, but that doesn't mean in practice it works like that.
The settlement doctrine, removal of Arabic as an official language, and language specifically about Israel being Jewish that were passed in 2018 are also instances where the law actually does diverge for Arab citizens. [1]
There's a pretty decent breakdown of why Israel officially meets the international requirements to be considered an Apartheid state here as well: https://www.youtube.com/watch?v=MknerYjob0w
Israel heavily disputed its responsibility to help with vaccination efforts of the same arabs of the territory it's annexing, so yeah, that's not great.
