Interesting question that's been on my mind, Mettaton says in the Genocide Route that Alphys safely and Quickly evacuated everyone to a safe place (Presumably the true lab) But if that's the case, why are there still 40 monsters roaming around Hotland? Muffet explains that she just flat out ignored Alphys but the rest aren't.
(undertale spoilers)
Mettaton never says Alphys evacuated everyone, but that she was “evacuating people to safety.” Whether or not she got to everyone is not something Mettaton ever confirms nor states.
The one who says Alphys would evacuate everyone is Undyne, but that was what was said rather than done. Considering the monsters that are found are random encounters, it’s possible Alphys just wasn’t able to run into all of those in time. She likely went for people she knew would be hanging around in certain places, such as Sans’ hot dog stand and the MTT resort. These would be the NPCs.
