This issue is found on various forums that are related to the Nikon cameras. According to some users, you have to manually connect the SD card to the card reader and transfer the files to your PC. Then after the files have been copied, format the card and insert it into the camera and Nikon Transfer will work again.
I've found another solution, but it involves fixing permissions for your Mac. While this is a good thing, it might break other stuff too, therefore I wouldn't recommend it.