> I run my gr alias for git pull --rebase to bring in the new changes

The mistake was blindly using git rebase. History rewriting (which includes not only rebase but also amend) should be done with care, and never on history which has already been published (with a few special exceptions, but unless you really know what you're doing -- don't).

The correct thing to do, since the commit was already pushed, would have been "git pull" without the --rebase, and then pushing the resulting merge commit. Getting in the habit of doing "git pull --rebase" every time is not a good idea; better have a "dirtier" history full of merges, than have to untangle messes like this one later.