GitHub emphasizes Pull Requests as a space for discussion. All aspects of it--comments, references, and commits--are represented in a chronological order. Rewriting your Git commit history while performing rebases alters the space-time continuum, which means that commits may not be represented the way you expect them to in the GitHub interface.
If you always want to see commits in order, we recommend not using
git rebase. However, rest assured that nothing is broken when you see things outside of a chronological order!