My daughter is 6 and she is complaining about bone pain to the point that is affecting her at school what could it be ?

Many possibilities: Take her to a pediatrician for an exam. That's the best first step. If tests are needed, follow through. If there is no physical finding, find a good child psychologist to help clarify problems she might be having with others in school, socially or even at home. Nip whatever it is early - her health and adjustment will be much better if you do.