Occasionally, bugs in either repository parsing or system configuration may result in phantom commits being visible in the Diffusion view (see https://secure.phabricator.com/T615#9). In cases such as this, it might be nice to have some mechanism to remove those phantom commits or to ask that Diffusion re-index the repository.
I'd imagine, from what I've learned about the internals of Phabricator, that this would be a fairly hairy operation - especially if there are existing audits on valid commits. It should probably be something done from the command line.