Focus only on points or in the entire box?

I started to notice some focus problems last Saturday when I was taking photos at my sister's bridal shower. However, I think I might have identified the problem and wanted to get some feedback from others. I thought I might have developed a backfocus problem on my Tamron 28-75 because I would focus on a subject and then a foot behind them would be in focus. However, I did some tests tonight and think (hope) I have identified my problem. I shot a subject that had a bad a foot in front of it and noticed that sometimes the bag was in focus and sometimes the subject behind it. I started to notice that the box was overlapping the front subject. I moved the entire focus box above the box and the focusing problem I had before seems to be a lot better.

When focusing, I assumed that the red dot was the only thing that calculated the focus. Am I wrong and the entire box surrounding the red dot is used for focusing?

AF is not only based upon an area of the 'entire box', but likely an area slightly larger than the box!

I was terrified that my lens was malfunctioning but I think the problem is that with my problem shots I was focused on an edge where 2 different planes overlapped. You have no idea how happy this makes me!