She wasn't supposed to be at the war in the first place. She was supposed to go with the Dandelions, MoM told her not to get involved with the Keyblade War. The fact that she did, and then didn't show up in KH3 is a major shift from the plan laid out, and is a result of Luxu going against what MoM said to do.
The traitor seems to be Luxu, and all signs in the game point to him as he bears the Recusant sigil (He has an X in his name unlike all the others, and later works for and becomes half Xehanort, who is tied to said sigil) he pretty outright goes against previously established orders multiple times, and he knows MoM's plans well enough to change them in the first place. I say this to explain why Ava being told this info is enough for her to break off. She wasn't supposed to know, and Luxu was told to stay away from Daybreak in the first place, and to keep his purpose secret. He's also shown at the end of the flashbacks questioning MoM's motives and methods, I wouldn't say it's too much to assume he's quietly rebelling.
Finally they were "called" to the future, and in the Keyblade Graveyard. The fact that they were called is hazy since we don't know where they were, but we do know that the last place they were seen was the Keyblade Graveyard, so there was no real change in scenery from our perspective, and if they came from after the Keyblade War, there shouldn't be any discrepancy in their eyes.