In case others come across this presently unanswered question (197 views on 2014Jul31);
I would't assume that clicking Smart Fasteners caused it. That might have just been the event which exposed it. Your next rebuild might have done it too. In my limited experience, "unexpected" mate or sketch problems usually have their root cause in a sketch (lots of other possible causes). A place to start is to verify that the sketch was properly defined, relations, etc.