Meg is unhappy at school in A Wrinkle in Time for several reasons. First, she feels she doesn't fit in. Her hair doesn't look right, she wears braces on her teeth, she isn't athletic and "normal" like her twin brothers, Sandy and Dennys, and she doesn't do well academically. One of her teachers has just told her that she will be held back if she doesn't start doing better:
Really, Meg, I don’t understand how a child with parents as brilliant as yours are supposed to be can be such a poor student. If you don’t manage to do a little better you’ll have to stay back next year.
Then, when she roughhouses, one of her friends tells her she is acting like a baby.
In addition, she knows the town is gossiping about her missing father and her seemingly strange little brother, Charles Wallace. As the story opens, she has just gotten into into a fight with with a boy from her school who insults Charles Wallace for being "dumb."
Overall, Meg is in early adolescence and feels awkward and like a "monster," which is not unusual for her age.