In practice and process PhD examination is distinctive, reflecting the high expectations of students whose learning has been directed to their becoming researchers. This article builds on previous research on the examination of Australian theses that revealed that examiners in Science (n?=?542) and Education (n?=?241) provide a substantial proportion of formative comment in their reports, much of which is constructed in a way that anticipates reflective engagement by the student. Detailed examination of the formative text identified nine categories of comment directed at three collective groupings of weaknesses or flaws related to less favourable recommendation. The flaws are related to "fundamentals", "project" and "argument". There were discipline differences, including significantly more comment in Science, indicating that the candidate should attend further to the data and analysis in their project and the fundamentals of presentation. In Education there was more emphasis on improving argument.