“Boys will be boys” might sometimes be true, but often it is not. If there were a small chance that someone’s food is poisoned, it would not be dismissed as quickly. If there is a remote chance that the occurrences observed are not “Boys will be boys”, there would need to be some increased observation, investigation, assessment, consultation, something to verify that there is nothing dangerous happening here. It is irresponsible and unprofessional for the school to be alerted to this multiple times, and to dismiss it with the wave of a hand. One cannot cry wolf for everything, but the ease of dismissing it is the opposite extreme, and intolerable.
As for begging for mechila, it is not quite so simple. The interpersonal asking and granting of mechila is a more complex subject than just a ritual of asking mechila. If it is not asked with sincerity, it is a sham. If the victim is not ready to forgive, because of the intensity of his pain, he cannot be forced to grant mechila. These are areas of halacha that are seldom studied, and may well be outside the scope of the kollel learning that somehow was allowed to become the prerequisite for employment in the chinuch field.
Forgiveness is an entire subject, both in halacha and in the professional world. It ain’t simple. It is truly a shame that such subjects are not taught in yeshivos, as they are pertinent to daily life, and should be a prerequisite for marriage.