Hmmm, I Have 2 clownfish and quite a few mushroom corals and havn't had any problems like this. Is your clown actually biting the coral and just pestering it? Clownfish have been known to host in a large variety of things besides anenomes, including mushroom corals. He may be trying to determine if thats where he wants his home to be.
I know my 2 clowns like on side of the tank more than the other and the bigger of the two will try to nudge or nip my habd if its on "her" side of the tank.
You might want to try moving the mushroom a bit if the clownfish keeps it up. Hope this helps...
Dew