Any question response can be configured as a "Not Applicable" response.
Just click the edit button for any response to a question, and you will see several configuration options.
Add Not Applicable response. This allows you to add a special response which the system will treat as "not applicable". With these responses, the system ignores any scoring you attribute to the question. For example, if you have 10 questions, each with 10 points, but at audit time you select a "not applicable" response, the percentage score will be calculated out of 90, rather than 100.
Note that you can name the response however you like (bearing in mind that you may be setting the questions up in a language other than English). When you select this option, whatever you enter here will be taken to mean "not applicable".