Altered Nova said:
Could it be that the exam actually involved three separate tests administered over several days, one for each of the three "core" e-rank jutsu taught in the academy (substitution, transformation, clones), and we are only shown the final of the three exams in the manga? This makes the most sense to me (why would they only test the students on one of the three basic jutsu that form the foundation of all ninjutsu?) but I have a hard time believing that Naruto failed the substitution and transformation tests. Clones are the only one of those three techniques he's ever been shown or said to have trouble performing.