コマンドが抜けてた
ffmpeg -i input -filter_complex split[0][1];[1]scale=-2:320[1] -map [0] -start_number 0 -vsync 0 -qscale:v 20 -qmin 20 -qmax 20 output1-%03d.jpg -map [1] -start_number 0 -vsync 0 -qscale:v 20 -qmin 20 -qmax 20 output2-%03d.jpg