Due to the wide variety of plugins and the various methods they can be implemented, its not possible for AEM Mobile to support all custom plugins.
I'm not overly familiar with the facebook plugin, but are a couple of patterns that we have noticed can cause problems:
App Delegates: Plugins that require reference to application-level classes, such as AppDelegate are currently not supported by the developer tools. This is because the application is not available when the framework is being built. The plugin would need to be modified to be standalone and not dependent upon AppDelegate. This would include any plugins that require access to AppDelegate.h or AppDelegate.m
Main View Controllers: Apps that require main view controllers (MainViewController.h, MainViewController.m, MainViewController.xib, or
main.m) will not work with AEM Mobile due to the fact that the Cordova Plugins are included as a framework.