My first iPhone 4 had this problem. It started happening about a month after purchasing it. I would click once and sometimes it would register as a double-click OR, because I have my accessibility options on triple-click, one click or two would register as three. Sometimes a double would act as one and so on. I restored from back up and problem persisted, I tried Set up as New, and it still happened. I thought it was hardware so I got it replaced. I restored from back up with this new phone and after a week or so, the problem came back. I got this 2nd one replaced 2 days ago, set up as a new phone and just today it brought the problem back again.
All these phones were on 4.1, so I think it might be software, unless I just have really bad hardware luck....