Yeah puncturing a roof is a big no-no - it can lead to water or structural damage to the house. Most companies (including ours) offer a warranty for it, and they did come out and fix it with some wood putty and paint, but we're still a little pissed. The also damaged the driveway (we're on a steep hill with a private drive, and told them that they can't drive large trucks up it, but they did anyway). And they seem completely incompetent for the first 2-3 times coming out and fixing it, until they finally gave up on subcontractors and sent their own guys out. CEO seemed to have no idea what was going on with his company with his underlings intentionally undermining him.
