Atom and Git pushing to remote


I am using Atom as my Git GUI. Git connects to my remote server via SSH. The server has cPanel installed with a git repository on it.

I have been using this particular git setup successfully for around 3 months now, I have had no issues pushing to the remote server.

Recently I pushed a large number of changes to the server (55ish commits).

Now I am noticing some strange behavior with git on the remote server.

Every now and then when I push from Atom to the remote server, the push is successful, however, git on the remote server seems to keep a duplicate of the commits within un-stage changes. To fix it, I have to clear out all the un-staged changes from the master branch on the remote server - really annoying.

Has anyone experienced this / have any ideas what’s going on?