Alan, your correct on the (2), (3) files.
Have had that happen to me as well, depending on what I had on the system at the time.
Additional areas that may cause problems, is if you have the same name file, but they are different.
Such as Defrag.zip & Defrag.zip.
Though you may have had 1 Defrag.zip on July 5, deleted it on July 6, then downloaded a new Defrag.zip from a different company, & when system restore commences, you might find that you now have defrag (1), Defrag (2) etc...
This could happen whether the Defrag.zip files were the same defrag utility, or an Auslogics defragger & an Iobit defragger, OR if they were both Defraggler from Piriform.
This example above is merely just an example to highlight the complexity of the problem, but definitely if you have a lot of files, be they zip, pictures, music, videos, EXPECT that if you have a lot (or sometimes even if you have a little) that some of them will definitely be confusing for System Restore to deal with.
Even if a Defrag.zip file has the same name, it could potentially be from 2 different defrag companies & thus have entirely different defrag programs themselves. Having a good backup is always good to avoid problems like these.
Without a good backup, you may be forced to sift through the same files you filtered earlier, the same files you deleted earlier, & have to re-analyze, re-delete, re-organize files that were once deleted getting dumped back in alongside files that are still present.