Just to check, I did a quick test on one of my systems. It worked as expected, keeping separate sets of edits for the two copies.
The next steps would be to see if there is corruption in your Photos library, something else in your user account, or perhaps something in the copy of the system on your Mac.
Test in a separate, temporary Photos library:
Export a few test photos to a temporary folder on your desktop if you don't have any loose photos handy.
Quit Photos.
Launch Photos again with the option key held down.
From the library selection dialog, choose the option to create a new library, with a test name and location.
Import a few test photos to the test library.
See if the problem exists in that library. (Duplicate a photo, edit each, check the results.)
If you don't see the problem in the test library, suspect corruption in your original library. Come back and ask for next steps.
If you still see the problem, try again in a newly created test user account:
Add a test account in System Preferences > Users & Groups.
Copy your test photos into the Public > Drop Box of the test account.
Log out of your normal account.
Log into the test account.
Repeat the test in the test account.
If you don't see the problem, suspect corruption in something in your normal user account (outside the Photos library, since you eliminated that above).
If you still see the problem, suspect corruption in your system software (or, less likely, your hardware).