Klein originally believed that the "Wishes" ability could be used freely as long as it didn't exceed a limit. To his surprise, the effects didn't solely come from the Beyonder characteristic.
To put it simply, a Miracle Invoker needed to seek out and satisfy all kinds of wishes before they could make wishes and personally grant them during battles, turning the corresponding situation into a reality. Furthermore, at the very beginning, the wishes that Klein could fulfill were small and trivial. He had to accumulate them one step at a time before he could create a true miracle. He couldn't do as he wished.