This is likely a problem with how you're structuring the HTML file. Make sure that the .html file you're linking to in the Web overlay is in a subfolder that contains only the files used in the HTML. If the .html file is in the Documents folder, for example, you upload all the contents of the Documents folder when you export the article. Put your html file in its own subfolder and try again.

I think it's a good idea to keep the same Bundle ID for iOS and Android. I can't think of any reason to use different Bundle IDs. In some cases, such as setting up Push Messaging in Mobile Marketing, using the same Bundle ID for iOS/Android provides more flexibility.

Do you get a gray app icon when you try to install the app? If so, the iPhone's device ID likely isn't added to your mobileprovision file.