How to reproduce:
- Develop is 6 commits ahead master.
- Create hotfix branch from master.
- Make 2 commits to on hotfix.
- Finish hotfix branch (merge to master, tag, merge to develop)
- Master is now 3 ahead origin/master (2 commits+merge commit)
- Develop is 57 ahead origin/develop (WHAT?!)
Why isn't local devleop 3 ahead origin/develop? I have a feeling it has to do with the --no-ff flag in the merges...
I had the same situation once. Since I had write access to the main repo I was doing the merge operations directly to upstream. That would cause some problems. So instead of doing the merge manually you must do it through a pull request, that is, push your Hotfix branch to your origin (your fork) then create a pull request from hotfix to master, after accepting the pull request the hotfix branch will be merged to master.
Now just open a pull request from master to develop.