Early on in the show, the Super Readers were prone to making mistakes while performing their powers. But as the series goes on, they typically go for the right answer immediately. This may be done for saving time for the show (and the later addition of Woofster) but perhaps the Super Readers are getting more experienced in using their abilities. They are kids after all.
So you got a bunch of heroes who can traverse fictional universes with ease and alter a story by replacing and changing words in the story's text. Seems normal, except when you consider this: You have a group of individuals who can travel to any fictional universe and permanently alter the rules, laws, events, continuity, objects, and characters of its reality by changing the very text its based upon! How does it feel to know that the most powerful character in all of fiction might not be an Infinity-Gauntlet wearing Thanos or a sun-charged Superman Prime, but a little kid on a show for elementary schoolers?
Why don't the characters just use their powers to fix the problem from the beginning?
Perhaps the powers only work in the books?
Because Storybook Village is sort of a "hub" so to speak, for literature, sort of like Game Central Station in Wreck-It Ralph is a hub for video games. Storybook Village is supposed to be a "safe zone" for literary characters, a place where everyone can relax and live comfortably without their own stories interfering with their free will. It's probably a rule that all Reality Warper characters, such as Super Why, should avoid using their own powers, lest the "safe zone" become unsafe.
Or even better. Super Why's power is the power to read and change words to solve problems. If Storybook Village is a free-will safe zone with no author, then that means there are no words to read and change.