This is an open issue in katello and Pulp, one of the backend dependencies. It is not yet triaged to an upcoming release since the fix is still being worked on. The issue stems from the old and new files having the same checksums. Because of this, the system attempts to de-duplicate content by reusing existing artifacts instead of creating new ones.
The workaround is to delete the old uploaded file, run orphan deletion and then re-upload the newer file. Please also note the setting Orphaned protection time which should be 0 if you want it cleaned up right away after removing the old file.