Had the same problem with an eShop download. Opening the manual resulted in an error "The SD card has been removed" even though there's nothing wrong with my n3DS' SD card/slot. Likely that the game doesn't work on the firmware version you're running. Try running it in emuNAND.
my brother has the same problem randomly too. it usually is fixed by removing the sd card and putting it back in. i've considered cleaning the contacts and rubbing in a little contact spray if i ever get around getting some.
I had same problem when I was using microSD Management with PC as I used my brother's faulty 16GB microSD, then I decided to swap my 4GB microSD back and it's fine.
Had the same problem with an eShop download. Opening the manual resulted in an error "The SD card has been removed" even though there's nothing wrong with my n3DS' SD card/slot. Likely that the game doesn't work on the firmware version you're running. Try running it in emuNAND.