I use the set up method where you use the SD card to boot and then a USB drive to actually run everything.
For me the versions of the software on the sd card and the USB thumb drive weren’t the same. Once I made them the same the issue went away.
If you’re only using the SD card, which may actually be plenty on a pi2, this wouldn’t be the solution for you.
Make sure you controllers are plugged in before you turn it on.
And try search for your specific controller on the forums to see if anyone else got them to work.
I was using the iBuffalo SNES USB controllers.