Other mistake: When Captain Underpants falls in the Turbo Toilet 2000's mouth which has a liquid in it, he doesn't turn into Mr. Krupp.
Continuity mistake: On the desk, Mr. Kurrup hits a big red button that keeps the boys locked in his office after they try to walk out. In the shot before, there is no button on the desk.
Answer: They never would have found him after CU slapped him far away. Plus Harold destroyed the shrink/grow machine so PP ended up permanently small, meaning someone could easily squish him if he tried anything evil again.