She's imitating Cueball's words, trying to grasp their meaning.
(Her words appear even at the same positions in the frame as Cueball's words did, letter by letter.)
The Beanish underlying the “yes” says “yes” indeed. From Cueball's repetition of her own repetition of Megan's word “cave”, Ms. Frizzle guesses (correctly) that Cueball's first word means “yes”.
The Beanish underlying “cave” does not begin with an interrogative prefix and does not end with a question mark any more. While Ms. Frizzle is still confused (thus the underlying gibberish at the beginning of “cave”), she understands that Cueball's sentence was not a question.
Summary: So far she learned the meaning of “yes”, “?”, and “.”, and that the word “cave” stands for something important.
