For safety reasons the application doesn't automatically delete anything it captures via the Internet Downloads capture method.
If JMR is detecting streams that are not media as you describe, then you can block their detection using the Adblocker. Settings > Advanced > Adblocker
Is there a setting to automatically delete completed recordings, when say, they are less than 5 MB?
This setting is very useful, as some streams eventually end up being blocked from view. When this happens, the Jaksta program freaks out and creates a 0 MB file every half second.