Are you absolutely sure those individual files are not symbolic links?
Rsync has a few useful flags such as -l which will “copy symlinks as symlinks”. Adding -l to your command:
rsync -rtvpl /source/backup /destination
I believe symlinks are skipped by default because they can be a security risk. Check the man page or –help for more info on this:
rsync --help | grep link
To verify these are symbolic links or pro-actively to find symbolic links you can use file or find:
$ file /path/to/file
/path/to/file: symbolic link to `/path/file`
$ find /path -type l
/path/to/file