Are you using a Bluetooth USB dongle? The Raspberry Pi Compute Module 3 doesn't come with Bluetooth built in. To connect your controllers via BT, you'd need to add a Bluetooth USB adapter that's supported by RetroPie/Raspbian.
Card Fighters' Clash 2 English Translation ( http://cfc2english.blogspot.com/ )
Neo Geo Pocket Flash Cart and Linker Project ( http://www.flashmasta.com/ )
Avatar art thanks to Trev-Mun ( http://trevmun.deviantart.com/ )
Neo Geo Pocket Flash Cart and Linker Project ( http://www.flashmasta.com/ )
Avatar art thanks to Trev-Mun ( http://trevmun.deviantart.com/ )