I've just noticed this for a couple of things after migrating to the Note 2.
Though there may be other causes I think it can happen if you mix and match copying via the phone and copying things to the card while it is out of the phone.
I also upgraded to a bigger, faster SD card and copied the contents of the old one on to it via a card reader.
If I copied a picture into an existing folder (Wallpaper was one) via the phone, either internally or via MPT then that folder would show twice. There would be a Walpaper folder showing all of the files and a Wallpaper folder showing only the new file and sporting a small SD card icon in the corner.
The solution full solution, if the problem persists, would then be to unmount the card and remove it. While dumping the contents onto a PC via a card reader force a media scan either with an app or by rebooting (I think plugging in the USB cable and unplugging it works too).
Once the contents are coppied delete them from the card then pop it back in the phone. Mount the card. Plug in the USB cable and put the contents back.