The issue of unfairness arises in high-stakes public examinations when students choose questions from alternatives that are offered and marks on the alternatives turn out to be discrepant. This paper addresses and defines unfairness and discrepancy in the context of alternative questions in Physics Tertiary Entrance Examinations (TEE) in Western Australia. As well, I present an analysis of question characteristics that explain observed marks-differences. The characteristics mainly relate to the construction of the text of questions, the detail on diagrams, and requirements for calculation. The list of characteristics could inform the setting of compulsory as well as alternative examination questions. The paper includes a brief exploration of results by gender on the alternative Physics TEE questions.