How are you trying to capture? Auto mode Im guessing as perhaps as the adaptive stream changes in your browser from low to high resolution both new streams are getting picked up, which is how we want it to happen. If so you can always cancel the stream you dont want.
If you are using the extraction method, entering the url, then onl the streams you double click on will be captured.
Please provide more details and debug logs as per https://www.jaksta.com/support/windows/technical/jaksta-media-recorder/how-to-generate-debug-logs-6000009063
when downloading from bbc iplayer i always get two files of the same program thus doubling the size of my downloads!