No guarantees, (there can’t be for any recovery attempt), but I think they are probably being ignored because they are the non-deleted files.
ie The files that were on the SD card when it was reformatted, which of course are what you want.
I think that you may have done the wrong-type of scan and recovered only the files that had previously been deleted.
But don’t worry, you just need to do a different type of scan.
There is a particular way to use Recuva to get those non-deleted files back from a reformatted drive, see this linked post.
(PS. if you watch the video linked in there the the guy on that is using a reformatted SD card to demonstrate the process).