The most common mistake is to attempt to add the tools directly without adding the behaviors on which they depend. The Navigation add-in has two behaviors which must be added: Navigation Behavior and Tool Manager Behavior. The Query add-in has one behavior which must be added: Query Behavior. In addition, the Query Add-in will not work unless the Navigation add-in behaviors have been added.
Other prerequisites exist as well:
The behaviors are not designed to work in Application Builder mode. They assume, upon loading, that they are in a fresh web session.
Inherit from the NavTool class. Download and study the code for the Navigation add-in for examples.
Application Builder acts buggy because it is buggy. The best practice is to use Application Builder only to create a new application, and then edit the config files manually thereafter.