It's not anything bald or very concrete. It's more like...the general feeling. I can give examples, thinking about it.
There's the obvious disconnect between Lunafreya's physical appearance between game and movie (plus miraculous change of clothes that isn't covered at all in-game). I think it's also that Kingsglaive seemed to be build up so much for the main antagonists (Ardyn, Iedolas, Ravus), when the game's narrative structure completely undermines or ignores them. Then there's the weird "they're magical, so go with it" thing of Umbra and Pryna being puppies during Prompto's Brotherhood episode while their age is consistently adult during the game (seen in the childhood flashbacks with Noctis and Lunafreya). And any emotional connection between Noctis and Regis is barely evident in the game, although it's palpable in the film and anime from different sides.
Of course some of this can be put down to each project's mutual dependence on each other (all parts are needed, or they fall down), but other elements just look like a different creative team who didn't get the memo.