BLTI-109 for a way to reproduce this. Ithaca has reported what looks like the same problem with Lesson Builder.
I believe the problem is in the way sites are modified. The code in DbSiteService.saveTx deletes the whole site and puts it back.The assumptions that if anything goes wrong, the transaction won't be committed. But depending upon the version of Sakai and Mysql, and the settings of parameters, the pool management code may end up doing a commit when recycling a connection. I believe the whole transaction should be wrapped in a try and explicitly cancelled if it is not committed.