Take a look at the sentence again:
At the back of the classroom, Nina sat with her arms crossed, glaring at
her teacher, Mr. Beane, her body language
indicated that English was her least favorite subject.
The problem occurs between Beane and her. Nina sat with her arms crossed ... begins a complete sentence. Her body language indicated ... starts the next complete sentence. Because these two parts have just a comma between them, they create a comma splice, a major sentence error.
To fix the problem, you could put a period after Beane and then capitalize the H for her.