It may take serious effort to determine if an application has significant unexpected or hidden functionality, and it would indicate deeper problems in the software development process. If the functionality isn’t necessary to the purpose of the application, it should be removed, as it may have unknown impacts or dependencies that were not taken into account by the designer or the customer.
If not removed, design information will be needed to determine added testing needs or regression testing needs. Management should be made aware of any significant added risks as a result of the unexpected functionality. If the functionality only effects areas such as minor improvements in the user interface, for example, it may not be a significant risk.