1) A lack of control groups. In fact, she was told by her instructors that many journals consider it an ethics violation to use a control group, the logic being that in denying your experimental method to the control group you're putting them at a disadvantage.
2) Overgeneralizing results. It's common to use education students (i.e, future teachers) as experimental subjects in education research. Then the results are interpreted as applying to all students, ignoring all the ways that your typical education students are different from your typical high school or elementary school student.
While there were some examples of good education research, she said that by far the best education research she could found was actually published in psychology journals. So it's not surprising to me that myths and even pseudoscience will proliferate in education when the standards on research in the field is so poor.