A picture showing the seals you're talking about would be great. But here is what I think you are looking at: Rubber roofs are sealed at the caps and around vents, tv antenna, etc with Dicor self leveling lap sealant. It's pretty standard to apply it in a very thick bead and with little regard for smoothness... the more the better! One of the things you may be seeing is the screws and rivets under the sealant. At least that's what it sounds like. This is absolutely nothing to be concerned about. And down the road when you go up to re-seal/spot seal in a few years, I would suggest you continue the trend of applying heavily on the seams. As I said... more is better!
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