Game Console Emulators for Linux

SuperNES

higan is the most accurate emulator, not the best UI and requires decent hardware though. snes9x is generally considered the best balance of being accurate enough but usable, Obviously would require more information to track down your issue though. Super Nintendo Snes9x emulator. Snes9x is one of the best SNES emulators on the Linux platform. It is very well designed, with a thoughtful user interface and tons of excellent features, such as gameplay recording, controller support, and various graphical enhancements.

Higan and Mednafen are both in Debian repos.

zsnes is considered outdated.