I ended up contacting FTPloy as I assumed that my problem might have something to do with the way FTPloy works. Here is what they said:
Git shouldn’t be initialised on your server if you’re deploying with FTPloy as we don’t have access to the .git directory on Bitbucket and only deploy your actual code. There are numerous security risks with deploying the .git directory so I won’t get into those now.
So, I'll remove the .git folder from my Production server and rsync Assets like user uploaded images to my local repo once in a while.