The reason that they get kicked out of the main hall is that Omri is making too much noise and Patrick is suspected of causing him to make the noise.
The situation here is that the school is having an assembly. In the middle of the assembly, Omri starts yelling "Ow!" Mr. Johnson is convinced that Patrick is doing something like stabbing Omri with a pencil because they are bored.
But what is really going on is that Little Bear has been stabbing Omri. He is mad because he's been kept cooped up in the dark of Omri's pocket. He wants to be out seeing the sights.