Without seeing some CSS and HTML code, it's going to be hard to help much. About the only thing I can suggest is to make sure that you aren't coding to a specific screen height in your app, and to double-check your viewport meta tag. Screenshots might also be useful in your case.
Well, the CSS and JS I'm using are from this plugin:
Here are two screenshots of my issue. My two buttons (intentionally gigantic LOL) are overflowed by Windows bar (back, home and search buttons).
Since you're using a framework I know nothing about, I'm going to suggest that you ask the developer. But it should be noted that the top of the page indicates that it is in development, so I wouldn't expect it to be bug free or ready for production.
Offhand it looks to me like your main content area is forcing a height larger than the viewport minus the size of the app toolbar. The "why" is difficult. As such in order to help you further, we're going to need to see at least some of your code -- please share your index.html and config.xml file (minus identifying information, if any is present) in addition to any CSS you are using, or post a link to your app so we can download it and see what's going on inside.