Earlier quoted context omitted.
On 1.: As others already noted, Git has a GC-mechanism, which means that objects can still linger around in any copy of your repo for a while. And if you need to version binary files, you'd better use git-lfs or git-annex. Obviously, if you don't need them, just nuking them outright with BFG or `git filter-branch` is fine, too. If you'd like to try git-lfs: It also includes tooling to retroactively migrate your Repos…
RE #2: (First, thanks for everything!) Our regular routine at the time: Imagine production and dev are even. We add 5 regular commits to dev. We PR merge dev -> production. We do not do squash and merge. We do not delete dev. Dev and master are now even but master has the merge commit as well. Flash forward several years. Looking at history, we now see each of those 5 commits for a run of about a year appear multiple…
I'm sadly still not all that sure I understand you correctly (and I'm afraid I can't tell you exactly what caused your issue), but:
If it is the commits that "do the work" that are duplicated (not the merges), I'd guess there already was someone (or some script/tool) that already rewrote history a couple of times and not everybody was aware of that.
If your team didn't look much at the history structure and try to actively shape it in a certain way, this could just have happened because someone did an innocent `git pull` after the history of the branch had been altered on the server.
`git pull` by default equates to `git fetch` and `git merge`, so if your history was altered, the branch would contain copies of the original commits (with totally new IDs), and git would "knit" the two copies together in a new merge. That means that this probably has happened around five times (since you see five copies of the oldest commits).
In this case, the hashes of the duplicated commits should be different. If that's not the case, I'd guess you have a client that visualizes the history in a weird way and the problem is something else.
Cleaning this up might then be more cumbersome, since the points you'd need to "adjust" weren't committed "back to back". If you're willing to do the work by hand, you could just string together intact pieces of the history into a clean one by using `git rebase` with `-r` and `--onto` (or `git cherry-pick`, but I've never used that one for complex topologies, so I don't know how helpful it is there)...