I noticed the clock discrepancy as well. But that's not it.
The moon (not Dalamud, and on that note, does the regular moon have a name too?) had normal phases, but it always appeared from dusk to dawn, as only a full moon would, regardless of phase. I noticed this at chance when I was in La Noscea and saw a 'waxing crescent' moon setting at dawn, when that particular phase should be setting in early evening. All other phase were the same.
I never noticed that. I can't recall the specifics, but the boat from Thanalan to Limsa seemed to move straight in terms of the compass. IE: You sailed 'west' into the sunset, but then Limsa appears on the horizon of the west, even though you should be approaching it from the east since the docks face west. (Or some convoluted mess like that).