Examiners and Instructors, for all their experience and professionalism, make mistakes. In your future flying career as a lowly FO you will see plenty of Captains making mistakes. It will be your job to point them out in a tactful manner and provide an essential back up.
During the course of my training I have experienced poor Instructors, biased Instructors and also those who just didn't like me (and made no effort to hide their feelings). I have felt short-changed and disadvantaged at times. However, I have also been trained by some extraordinary pilots and others who go the extra mile.
People who join training departments within Airlines or Aviation Authorities are from mixed backgrounds, with a variety of motives. They are not necessarily good teachers or good judges. Some are exceptionally good. Even they make mistakes.
But all in all, I think Zondaracer has a good point. Where a candidate makes a number of minor errors and the Examiner feels they have fallen short of the required standard they must hang their hat on something. Like the time I got the cane at school on the occasion it was actually somebody else talking in class, sometimes you get what you deserve for the wrong reasons.
If you can honestly say you deserved to pass and the mistake the Examiner highlighted was your only potential fail item, appeal. If in doubt, perhaps take it on the chin. As long as you can learn from the incident, you'll improve as a pilot.
Hope that helps.