A question that I answered earlier today is mysteriously absent from the Top Questions list when I visit the site. However, if I search for the question using keywords, and click the "Newest" tab, it appears right where it should be. I am not familiar with this behavior -- is it normal? I do see that the question currently has a vote score of -4 and one close vote, but I don't know if that accounts for what I am (not) seeing.
Questions are dropped off the Home / Active tab once they reach a score of -4 on Main, or -8 on Meta. Since you mentioned that the question on Main that you were monitoring had a score of -4, this is most probably why it was no longer showing up on the Home page.