I had to look it up and Alice's eye color is... remarkably inconsistent. It appears as yellow in Mystic Square, then sort of greenish-yellow in Perfect Cherry Blossom, then orange-ish in Imperishable Night (although I'm not sure if that's an art thing or a plot thing), then green-ish in SWR and Soku. Alice only started to be depicted with blue eyes in some of the print works like Grimoire of Marisa.
So what I can tell the answer to Alice's eyes being yellow is "you can draw her with pretty much any eye color and it'd be correct at some point or another"
