Board Thread:General Discussion/@comment-32182236-20181101220519/@comment-31536324-20181103230349

I don't know what to make of it. Still don't see why the anomaly can't just be Frisk, doing the saving and loading... But this is a later iteration. You see, we can actually mention that Sans is supposed to know Toriel, or that Undyne is SUPPOSED to know Alphys. It seems as though we have deja-vu moments of the original Undertale. Perhaps Kris and Chara do as well."

As mentioned in said post, the end of the Pacifist Route establishes Frisk as their own entity, separate from the player. Same with the end of the Genocide Route for Chara. Yeah, Frisk is the one with the power to SAVE, but it's ultimately the Anomaly pulling the strings, with Frisk none the wiser.

Frisk, after all, is pleaded to be let to live their life by Flowey. He likely THINKS Chara is the cause of the RESETS this time around, but is unaware of the bigger fish in the pond.