How did this happen?

Yesterday Alfonso was walking out and about in my town and the next day he moved out!

I did Time Travel, but only several hours. The situation was, that yesterday I was trying to get enough bells to buy the throne. I was tired of playing so the next morning, I traveled back, readjusting the DS clock. Not the in-game clock. It was night time and I was walking past Alfonso house and the lights were on. I didn't check inside, because I saw him walking earlier to the same day. Then I time traveled to the present day, adjusting the DS clock again.
I open my mailbox and received a letter Alfonso saying that he moved out!

WHY CAN'T Samson or Eloise move! Why is it ALWAYS the villagers I want to keep!

If you go back a day it counts as one day, so what I assume happened is: 1st day, you play and then go to sleep. During this day Alfonso is walking. During your sleep the clock goes over 6am so it changes to 2nd day. Then you go back to day 1, which counts as a 3rd day. During this Alfonso is in boxes. And then you go forward one day, now the 4th day even though the date is technically at 2 and Alfonso moved out.

Just be sure to check your movers every 3 days or so to be sure and remember that going a day back does count as a separate day.

What I assume happened is that you either accidentally messed up AM/PM and went back a lil too much or you tt'd from 6 am to an earlier hour.

Yeah, travelling backwards is generally a bad idea. If you're going to use the DS clock instead of the in-game one then travel backwards, why bother? If you're going back in time, the game knows you're travelling.