We had our yellow striped maroon clown host in a frogspawn as well as a bubble coral for a while. Aside from the coral not opening as much as usually the fish was hurting itself. Its face and belly were all scratched from scraping on the skeleton of the coral.
I would try to discourage your clownfish from doing this. Whether you sit him down and have a little talk
or just move the coral a few days in a row (he'll get confused) is up to you. I would do something though so the fish doesn't scrape himself and have it get infected or worse.