We have an issue but I believe that it might be related to how we are making our changes. Basically we are seeing the non-conflicting merges in the remote git branch that the local git branches are making.
We are running the following commands
git clone remotebranch local
git checkout localBranch //make change is localBranch
git pull remotebranch // merge happens but not in a file local developer is working in
git commit -m " changes"
git push // merge shows in remote branch