Team 7 was formed under the basis that the top student was paired with the bottom student, according to iruka-sensei, but naruto must have been scored on his performance in the battle against mizuki since that's why he earned his headband. If the exam was on cloning jutsu, how did naruto get the lowest score with hundreds of perfect shadow clones?
I have another issue with this episode, too. Later in the series, it is stated that the scroll would be useless to mizuki since it was encrypted so that only jonin could understand it, so how did naruto learn from it? I'm quite far into shippuden at this point so I have no idea what episode that was stated in, so please correct me if I misremembered.