The iBuffalo USB SNES controller issues are rather common, particularly in RetroPie and with ZSNES.
Several users in various forums (too many to cite specifically) report ghost button presses and the turbo function jacking up certain buttons.
From the RetroPie Forum wherein users are stating issue with iBuffalo pads specifically:
(From forum poster, 'gravvoid'
I was getting this issue with the iBuffalo controllers but I somehow seem to have fixed it.
I went into the emulationstation config (/opt/retropie/configs/all/emulationstation/es_input.cfg) and removed the controller config for the controller entirely.
I went back to onto my actual Pi after rebooting and set it up as a new contoller. Now it doesn't skip though the menus at all.
The only difference made to the config file really, is that the iBuffalo input config is now at the very bottom of the input list instead of being the first on the list.
I don't know or understand why this has made a difference but I'm not getting any ghost inputs at all. I've currently left it for over 2 hours and there's been no movement.
While he's specifically talking about ghosting, the general consensus is there's a problem with some controllers and the way RetroPie configures them and with the internal hardware of the iBuffalo (crystals) in some cases, making the combo a frustrating experience for some. Your issue is exactly this mix.
A more in-depth explanation of how to adjust things in RetroPie using the RetroArch configurations is on their github, here.
I haven't delved into the setting on that level, yet, for controllers.
Logitech F770 is what many are rocking and by all accounts, is well loved for its total lack of issues.