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; and this affects on productivity, wasting of time of QA team if needed in functional/regression testing. Can Management team should be aware and take any added significant risks as a result of this unexpected functionality.

How much it will costs on QA, management and overall productivity of an application?

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; and this affects productivity, wasting of time of QA team if needed in functional/regression testing. Can Management team be aware and take any added significant risks as a result of this unexpected functionality.

How much will it cost on QA, management and overall productivity of an application?