Solidworks is Cutting a larger area than I want

I basically extruded a rectangle in Solidworks (2011) and wanted to cut out the center portion of it, so it leaves me with two small extruded rectangles at a distance apart from each other.  I know I could have drawn this differently.  My model has been fine for the last couple weeks and while I am editing my drawing today a portion of the model is now cut out, as if I had drawn a rectangle and extruded cut through most of the part.  Help is appreciated. Of course this would happen as I finish up my work. I ended up closing what I was working on without saving and restarted SolidWorks. This seems to have fixed the issue, but why did this happen?

SolidworksDrawings And Detailing