Here's what happens:
* The boys arrive late and noisy. They are full of energy and excitement, and their arrival is a distraction to the proceedings.
* They whisper and giggle. They are not paying attention to the examination and instead are busy talking amongst themselves.
* They throw paper wads. Tom Sawyer and his friends engage in some lighthearted chaos by throwing paper wads at each other and at the schoolmaster.
* They create a diversion. When the schoolmaster tries to regain control, Tom and his friends start a commotion by getting up and "marching" around the room, distracting everyone with their antics.
However, the boys' actions are more about playful mischief than malice. They are not trying to cause any real harm to the schoolmaster, they are simply having fun and being disruptive. The schoolmaster eventually loses his temper and sends the boys out of the room, but the scene is more about lighthearted chaos than actual harm.