In El Capitan, how can I prevent the Mac bluetooth mouse from from 'carrying' its scroll between different elements on a single page?
Actually, this is not a thing you can fix on the operating system as technically you still are using the same window/part of a window which is a web view (in whatever browser you are using).

This can only be really fixed by the webpage itself by not making some elements scrollable. For example it's possible to deactivate scroll-zoom in some map providers widgets.

I'm sorry to say that you may not be able to switch this off on an OS Level. Depending on the web browser you are using, there might be an extension that forces to turn scrolling off for some elements but that would most likely lead to partly unusable web pages if you ever need to scroll some of these elements.