That depends on how the game handles advantage during combat... does it actually roll twice or just add a flat +5 bonus? If it's the latter it's not really surprising the Githyanki hit you (they are +9 to hit in PnP and I suspect in BG 3 they might be buffed).
Also, what armor type did you wear? It's quite possible that there's a homebrewed mechanic that lowers your DEX bonus to AC when paralyzed. If you're heavy armor that obviously shouldn't matter, but still...
Of course it's also possible that you were affected by a bug.
