I suppose as a "cheap" way of doing it, you could:
1) Convert both clips into individual frame images.
2) Compare using an image comparison program, ideally one that would just output a report - if all
the images in the shorter clip compare at, say, an 80+% match with some of the images in the other - chances are it's a clip cut from the other, (either it or its source).
Downside is it will be hugely resource intensive in terms of space, time and CPU/GPU.
Here's a script on Ubuntu, (and a link to a Ruby version in the last post), that will compare exact same video across different formats/framerate: Script to find duplicate videos based on content regardless of format.
- it might give you some ideas.
There's also UQLIPS
, (video upload/search link): A real-time near-duplicate video clip detection system
(PDF paper) - who knows, they may be working on a standalone program.