Hi Divyanshu,
I tried to replicate the scenario in one of my test machines. then referred to the PPM database.
The PRNOTE table shows something like this:
Note 4 and Note 5 have been created by me from New UI. And the PRUID seems to be a bit different, unlike the ones that were created from Classic UI.
Check if the problematic Notes that you can see in the DB are created from Classic UI or New UI.
Do you have any custom processes internally which runs on the Timesheets and add a note to the Timesheets? Just a thought.
Thanks,
Abhisek Dhar