I'm talking about the presentation of the story, not petty, immaterial things like whether Ether got renamed Tincture. The only place I can think of where it was actually compromised was Celes's suicide attempt, which got nonsensically rewritten as a "leap of faith."
Things like translating Relm's dialogue as referring to herself in the third person are true to the letter of the Japanese version, but they either carry different, unintentional meanings or make no sense at all from a Western perspective. They've been translated without being localized.
(In the example given, in Japan, using the third person to refer to oneself is associated with small children; for us, it's how cavemen talk. The competent, official localization makes Relm use normal pronouns while finding ways to convey her childishness that still makes sense in a Western context.)