Might could be just because they were irritated by him sitting on them. I've had a green clown goby for a few months and have never seen him nipping at any of my SPS. He likes to hang out in my digitata, which at first retracted its polyps in response. But now the coral seems to have "gotten used to" the goby and stays polyped-out, even when he's lounging among the branches.
They're neat little fish, but very susceptible to ich. Mine was originally one-half of a pair, but his mate never fed well and died not long after being introduced to my tank (the current one recovered and is doing fine). Make sure the goby is eating well, monitor him around your corals (at least initially), and watch him carefully for signs of ich. Good luck.