I think that Phabricator does not correctly handle git merge commits. In my particular case, I am experiencing the following issue...
I had set up a Herald rule so that if anyone modifies an .arclint or .arcconfig file, it triggers an audit by myself. Now, I have a bunch of audits waiting for me because people merged a change that I had made to the .arcconfig into their branch, which was later merged back into master.
i.e. Someone is working on a branch X and merges master in X (bringing with it a change to the .arcconfig). Later, branch X is merged into master and I get triggered for an audit.