Sadly, Git users frequently do rewrite published history, by merging branches via "git rebase" followed by a fast-forward merge (i.e. replaying the branch on top of the target), all to maintain that wonderful linear "history". And that's a bad thing because it destroys information about the context in which a change was made. (I've been baffled a few times by apparently bad commits, before realizing they were rebased and did make sense originally.)
If they're rewriting published history, it's even worse than that, because it could change history that you are currently developing on top of, requiring some more advanced git knowledge to get your local repository into a correct state.
I have not found it to happen often though, for two reasons. First, it is widely agreed upon among almost all mildly experienced to highly experienced Git users that rewriting published history is a bad thing. Second, if it becomes a problem with new Git users doing this, you can turn of non-ff updates in the public repository, thereby disallowing this to ever happen, unless you go through all the steps to delete and recreate a branch.
If you're working with your local unpublished history, then it is your responsibility to make sure they still make sense in the context of newer updates from the public repo regardless of whether you rebase or merge. I can see how it would be confusing if people failed at this. I tend to find that more confusion results from people inflating the history with loads of one-commit merge bubbles everywhere rather than just rebasing their small changes.
