Why is ffmpeg outputting a 600fps video from a 120fps video input?
Update: The PTS entries of the input and output for the command below are identical in version N-79630-g9ac154d. Looks like the file is falsely flagged as VFR. But this single-step command below works for the sample video.

Use

ffmpeg -i input.mp4 -vf "crop='if(gte(iw,ih),ih,iw):if(gte(ih,iw),iw,ih)', scale=640x640" \
   -an -c:v libx264 -profile:v high -level 4.1 -preset veryslow -crf 20 -vsync 0 output.mp4




The framerate stored in the container (tbr) is 600, whereas the reported fps of 118.99 is arrived at by counting the number of video packets and dividing by the total duration. If this is not a variable frame rate stream, then add -r 118.99 as an output option.



For older versions,
Alternatively, output to MKV i.e.

ffmpeg -i input.mp4 -vf "crop='if(gte(iw,ih),ih,iw):if(gte(ih,iw),iw,ih)', scale=640x640" \
   -vsync 0 -an -c:v libx264 -profile:v high -level 4.1 -preset veryslow -crf 20 output.mkv


If you then mux the MKV to MP4,

ffmpeg -i output.mkv -c copy output.mp4


The resulting MP4 will show (close to) the source framerate.

Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'no-rc.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 512
    compatible_brands: isomiso2avc1mp41
    encoder         : Lavf57.34.103
  Duration: 00:00:02.75, start: 0.000000, bitrate: 2462 kb/s
    Stream #0:0(und): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 640x640, 2444 kb/s, 119.88 fps, 600 tbr, 16k tbn (default)