It's not really direct lies, but lies of omission. She uses peoples' ignorance of her true nature to present herself as a goddess and task people under that false pretense with combating the Ascians and their influence. Further she's not exactly forthcoming with the truth (for whatever reason), and Emet-Selch implies if not outright states she covered up the history of Amaurot after the Sundering. (Why? Who knows.)
The possibility that neither Hydaelyn nor Emet-Selch are lying about anything isn't lost on me. There are ways to reconcile their conflicting viewpoints. That said we don't have Hydaelyn's side of the story - but we do have a reliable (though very biased) expositor on the history of the world pre-Sundering whose claims are pretty well backed up. I don't think Hydaelyn is necessarily lied about that but with the information presented in Shadowbringers... yeah, she kinda did.