Britishguy,
There are essentially two ways in which questions can be challenged. The first is by the students making a comment on the scrap paper provided in the exam. The second is by the FTOs who have until the end of business on the Friday of the exam week, to register any problems reported to them by their students.
The reason for this tight timescale is to enable the examiners to consider, and decide upon all challenges before starting to mark the papers. So whatever mark you receive in your exam results takes account of all challenges lodged.
If a challenge is accepted as being valid, the question to which it refers is temporarily removed from the question bank and the marks are awarded to all students who took the exam. The subject question is then examined by the appropriate JAA committee at a later date. Defective questions are either scrapped or modified, before being reused.
The best way to deal with problem questions is to lodge a challenge at the end of the exam, then report the problem to your CGI. He can probably make a more reasoned argument which has a better chance of being accepted by the examiners.