If you use persistent variables (/set %varname value), that's always a distinct possibility. None of my scripts store data in Variables (except possibly during development or while a section of the script is in progress). One way you can avoid that is to use an .ini for your $script and store your data inside the same file as the script itself. When you unload the file, you unload the data; when you reload the script, the data is still there, already loaded as well. Or you can store all your script data in a hash table that your script loads on START from a file with an odd extension.
If you used a single section of the registry to hold script data, you'd be sharing that section with every other script, so the same thing applies there as would apply to persistent variables.