I guess I fixed it, but I had to change my script so that it re-encodes the video clip instead of copying. It's a bit slower but much more accurate now.
`ytgif -v -start 1:58 -finish 1:59.9 -caption "damn you" 'https://www.youtube.com/watch?v=tskpXGAJMhw' damn.gif`
https://github.com/llimllib/ytgif
To ffmpeg I say (in the nicest way):