Issue with Retroarch

[Timoboy]

Hi guys so for about a year now im into emulation, slowly building my collection of games and systems. So yesterday i thought it was time to step it up a little bit. for the past i've been using a ps4 controller to control my games. I had a idea to buy system specific controllers. so yesterday i bought a usb nes controller and a snes controller. So while is was setting up i notiched that for one system it worked but once i changed the controller and system it all got messed up again. so thats where i find out asbout custom configs. But now a other problem pops up. i've got all the buttons that are needed mapped properly and saved to the right config but somehow once i go ingame all the buttons mess up again. for example i just have my nes controller mapped as button b to button b button a to button a ect. but ingame button a is fast forward and my start key is exiting the game . I only changed the buttons that where needed everything else is still default.

What did i do wrong