Some uploaded packages do have these backup files within them but the majority dont.
This may have caused the initial duplicate warning.
As for your thought @Andreas_Dieckmann this appears to be correct.
I have multiple users accessing scripts that do use nodes authored in older versions (1.2 being used in 1.3) which exponentially adds to the duplicate warning problem. Each time a user runs my script (possibly 5 times in an hour) a backup is made for them. So 5 users over the course of an hour have created 25 back ups!
My script that clears these backups works fine, but i have the feeling my IT department will need to pur a task in place to do this more regularly… 
EDIT: Here is the code content of a simple .bat file that can be run on PC startup to perform the same task.
(Obviously adjust the directory path to point to your packages location)
cd /D P:
cd Drafting\Dynamo\Packages\
del /S *.backup