Unfortunately there's not enough information to be of much help. :-(
1. Share your index.html, index.js, and config.xml (or links to them). Strip any identifying information you don't want public.
2. Share what the script is, how you added it to your app, etc., and how it fails in the downloaded APK (error messages, console log messages, etc.)
3. Share what device(s) and operating system version(s) you are testing on, as well as any plugins (and version#s) you are using.
That would help tremendously.