The thing that bugs me the most about Alphys’ and Sans’ dialogue in the pacifist ending is that, to get that ending we had to get Alphys to tell everyone the truth about the amalgamates and teach her how to stand up for herself and her actions and be honest. But then, when we think she’s finally come clean with everything:
Undyne: “Oh man!!!” “We’re gonna be able to watch anime online!?“
Alphys: “Of course, Undyne!” “What do you think we’ve been fighting for all along?"
Sans: "yeah, what do you…” “whoops."
Alphys: "Jinx!” “I knew you were gonna make that joke!"
Papyrus: "WAIT, ALPHYS, I DIDN’T KNOW YOU KNEW SANS."
Alphys: "Well… I…"
Sans: "doesn’t everybody?"
Like!!! We talked about this, Alphys!!! This is exactly the sort of thing youre not supposed to do!!! All of our work and support didn’t do anything!!! How dare you!!!
Actually, I appreciated this for almost the exact same reasons! Changing behaviors you’ve had for years isn’t as simple as flipping a switch. It’ll take time for Alphys to get better at being honest all the time. Though I will also note that whatever’s going on there is also Sans’ secret, and there’s a big difference between not keeping your own secrets and not keeping someone else’s.