Reaching the overall pass mark is necessary but not sufficient. You must also reach aminimum in every scoring section: 19 out of 60 for each section at N1, N2 and N3, and 38 out of 120 in the combined Language Knowledge · Reading band at N4 and N5, alongside 19 out of 60 in Listening.
So an N2 candidate can score 97 out of 180 — seven points clear of the pass mark — and fail because listening came in at 17. It happens every sitting, and it is almost always listening, because listening is the skill that responds to hours rather than to revision.
The JLPT also uses scaled scoring. Raw marks are converted through an equating process so that a given score means the same ability whichever paper you sat. One consequence: you cannot calculate your score by counting correct answers, and a practice-test percentage is a diagnostic rather than a prediction.
Full explanation of JLPT scoring →