You can't measure energy in terms of mass and volume, you can only measure mass in terms of mass and volume. So the teacher was absolutely correct. (While Magic School Bus might have had a mistake).
If a student made a mistake, and a teacher went along with it, then every child in the class thinks that the mistake is a true statement... So I see no other way but for the teacher to say "sorry, <insert student's name>, you are incorrect, matter is NOT the same as energy".
Are they related? Sure! But so are many things in the universe.
D=S x T
Distance = Speed x Time
Does that mean Distance is the same thing as Speed? or Time? Not really... They are related, and they affect each each other, but they are not the same.
Matter can be manipulated to release energy, while energy can not be manipulated into creating matter.. i.e. you can't take light and create light bulbs, you will need glass (matter), wire(matter) to release the energy. "Release" does not equal to "create".
Pride set aside, if you do read up on the subject, or contact a professor teaching physics, of course he'll tell you matter and energy are related, but he/she will not tell you they are the same. If you decide to research it, then it would only be right to let your daughter know that she either misunderstood the book, or the book does have a mistake (which happens as well).
Going back to the general question you asked, if the teacher DOES make a mistake, then there is absolutely no harm in sending in information. If you have questions regarding material being taught, and need clarification, then there is nothing wrong in getting that clarified either.
The only concern I would have in this scenario is why my child feeling disrespected when she is corrected, and if the teacher made fun of her, or what exactly went on. Either the teacher needs heads up on treating your child with more respect, or your daughter will need to understand that it's ok to make mistakes, and that if teachers didn't correct mistakes, then kids would learn wrong information.
Good luck on either decision.
P.S. If energy equaled matter, then the formula would go "E=M". "Same" and "equal" are very definitive words, and energy does NOT equal matter.