I'm surprised you don't know the difference:
https://forgottenrealms.fandom.com/wiki/Githyanki Githyanki's hatred for mind flayers is explained there and by the other posters above. Basically, nobody knows what world githyanki came from, they don't even know that, for it's knowledge has been lost to them, because of the millennia they spent being enslaved by the illithids. And, they both use psionic attacks, it's natural for mind flayers to use them, while gith (yanki and zerai) honed these skills to eventually turn them against the mind flayers. Also, like some posters mentioned above, the githyanki are massive hypocrites, for they hate mind flayers for the long years they spent being enslaved, but see absolutely no problems in enslaving other races.
And there of course is that
small detail of mind flayers being a parasitic race, after all, in the FR, souls and gods are real things, when someone goes through ceremorphosis (you should really see the tadpole as a parasite) at the end of that process, the host's soul is completely destroyed, a 'fate worse than death'. Also, your soul also gets slowly destroyed in
https://forgottenrealms.fandom.com/wiki/Wall_of_the_Faithless , basically, again, after you die, your torment truly begins in some cases.
