Disable bilinear filter: Under system “retropie” you can find “Edit RetroPie/RetroArch configurations”. Run this option and selet “Change common RetroArch options”. Select “All”. Now disable “smooth_video” and close menu.
Disable hardware upscaling: If you launch a game press a button (or x/m). Launch menu pops up. Select option framebuffer (fb) resolution. Select framebuffer resolution = native resolution.