I had a situation at work where we have a git repo with ~80 active users working on.
There was a commit #1 on feature branch modifying a file. Branch was merged into master.
Some later time I have found that change introduced by commit #1 is missing on master.
So I ran git bisect
pointing commit #1 as good and current master as bad.
After some steps git bisect found that the commit to blame for the loss is some commit on another feature branch made months ago touching completely different code area.
I ran this bissect again and again and again. I have also asked my coworker to do it. Every time the same commit was comming out.
There is no way we could explain this behavior. It is extremely hard to investigate history and file changes manually as history is very large an complex with many many merges between branches.
Recently my coworker had similar problem with another missing piece of code in another code area. And once again bisect blamed unrelated commit.
I am completely clueless about what's going on.