Has anyone else seen bumps under the rubber roof? I had some warranty work done that involved the AC and I don't remember seeing them before but this was the first time I had washed the roof. I'm thinking this will become a problem as they will wear through the roof eventually.https://goo.gl/photos/HLnJzvMuV8fKLm9a8
That looks like nail heads backing out of the wood below.. They are evenly spaced and may or may not cause you problems unless they are walked upon.. I definitely would bring it to the attention of the repair shop who worked on your AC and ask them to fix them.