[Carl n Susan]

My first thought is you rubbed the roof on a tree branch without realizing it. That is the cause of most of the rubber roof holes and tears. Staples popping up are rare and you will see them sticking out if they caused a hole. The answer is to get some Eternabond tape, clean the spot, apply it and forget it (until the next hole/tear). We have all done this and Eternabond is your friend.