The preview for rename scripts like that may be inaccurate, since the script checks the files on disk and the preview is generated without actually renaming anything, so the files on disk haven’t been changed.
This is mentioned and explained in more detail on the post about the script:
Note: The preview in the Rename dialog may display several files with the same number. This is normal and does not reflect what will happen if you go ahead with the rename. (The reason is obvious: The script works by testing whether the names already exist on disk but just doing a preview doesn't rename anything, so the filenames in the preview do not affect each other like they will when you do the rename for real.)
What happens when you run the actual rename?