Twitch vod downloads from the Creator Dashboard are all variable frame rate (VFR).
You will need to convert all videos to an Edit-Friendly state for Shotcut.
These are screenshots from your video:
You have two different frame rates that Shotcut will be reading.
In your video, you swapped one video out for another one, yet didn’t change the Video Mode.
I would be curious to know what your Video Mode is set to.
Using MediaInfo to show video details, this is a file I downloaded last year from Twitch.
It was streamed at 30fps.
It’s in the range of the minimum and maximum as indicated with MediaInfo.
I also have the color transfer properties intact.
When you convert it to an even frame rate of 30.000000 fps or 60.000000 fps, it will drop/add frames as needed, but the file will be much easier to edit.
For future videos, I highly recommend only recording with OBS.