Adding credence to the 'Melia is Maria' theory is a rather prominent omission during the Kugearen City arc: the player investigates the Theolia household with Kanon and Venam- but not Melia, who doesn't get involved until the bomb scene. It's entirely possible that if Melia is Maria, seeing her parents and her old self would have had unforeseen consequences.
.Karma Files shows us a Bad Future where space warps around and time doesn't flow. What could cause such a thing? Well, maybe the Renegade player and M2 killing Spacea and Tiempa could have done it...
In Kreiss' secret scene, he tells Martin that Angie actually treated him quite well while he was imprisoned, but he doesn't know why- evidently Angie never said anything about her being his mother. This actually makes perfect sense after playing Anju's quest: As far as Anju- and thus Angie- knows, Kreiss should still be a baby, trapped in her ice with her parents, and when she froze him, nobody knew about it or had the means and motive to free him. In addition, Spacea and Tiempa had Kriess raised in Galar, fifteen years before Anju froze him. Ergo, Angie was confronted with a man who had the same name as her son and the family resemblance, but was too old to feasibly be her son (as far as she knew) and had a Galarian, not Aevian accent. She might have suspected that he was her son but had no way of finding out for sure, or she might have just been nice because he reminded her of her son, but in all likelihood, she doesn't know who he is either.
If you change your appearance to one of the other player characters via Mr Luck's contract, everyone still recognises you. Gameplay and Story Segregation? Nope. Everyone sees you as a random one of the A-team anyway.
Angie sucks you into her world using a Dimensional Rift. As far is we know, Zetta's the only one with the power to control Dimensional Rifts. Since Angie isn't part of Team Xen, where did she get a Dimensional Rift from?
Seeing as how Vivian was reincarnated as a human Dimensional Rift after botching a Garufan ritual, it's very possible that the Dimensional Rifts (and, by extension, rift matter) were originally created by the Garufa.
During the raid on the Wispy Laboratory, you battle a bunch of grunts who beg you to stop, claiming that if you interfere "things will only end bitterly for [them]". Then you find out what Madame X does to people who fail her, killing the ones who are no longer of any use to her. Who wants to bet that the grunts got "fired"?
Which also casts a dark light on a grunt exclaiming "I want to live!" before you battle her in the Wispy Laboratory. She doesn't want to get killed for losing.
