I don't know what to tell you about how this happened. It is definitely concerning for any files that change without being noticed.

I pulled down the latest change from what is our project's master branch which I will just call master(Sourcetree). I then created a branch off of our master branch (Bit Bucket). I think checked out the new branch in Sourcetree(BitBucket->Sourcetree). I modified my files and thought one of them looked off but I didn't know enough about it to make any changes to it and pushed the changes to origin(Sourcetree->Bitbucket). Next I opened a pull request and got it approved as all the changes were what was needed(Bit Bucket). I then conferred with my coworkers about the file that was off. There were a bunch of changes shouldn't be there as they were backed out months ago. Looking into the history of the file the commit before mine had all the changes backed out. There was a significant mismatch between the two versions. The problem is that the diff only recognized the changes that I had implemented. and ignored everything else that changed. It even showed in blame that the changes of those lines went back to their original commit instead of the one that fixed it.