>>2062
Yes, losing some challenges shows this (get hit by the lasers, don't defuse the bombs in time, etc), and her dialogue in the core about her map being wrong also pretty much cements it. She also claims that she did it to persuade you not to go fight Asgore, but it's made clear by her behavior that she uses that as more of a guise for her need to self-insert as a hero into your life.
The only legitimately "bad" thing to happen to Alphys was Mettaton becoming distant when he became a TV star, but one of the Neutral ends shows he still very much cares for her and regrets this. In the True Pacifist victory lap you can see Metta reconnecting with Napstablook, so it can be assumed he would do the same for Alphys, one of his only true friends.
She gets no consequences for her wrongdoings because "waaah she's guilty and depressed". By no means should Undyne have been okay with the Amalgamates. And on a more meta note, she ruins the flow of Hotlands immensely with her annoying phone calls. I don't understand why anyone likes this character, even Toriel's lack of punishment is easier to stomach than hers.