First and foremost, disable the hardware decoder and try again. There is a high probability that will correct all your issues.
If that doesn’t work:
Are your video files variable bitrate? Try converting to edit friendly and see what the output looks like?
Can you please:
- Show a screenshot of your timeline from within Shotcut.
- Attach a copy of the project file (.mlt)
- Either link to YT or upload a part of the video output that is misbehaving.