Review the Student Account to see how the Pell was applied. Usually grants are applied to qualified expenses first, but you need to review the details.
Is box 5 greater than than box 1, which is eliminating the credit for the parents? I'm not sure from your question, why the AOTC is not calculating.
The Pell grant was larger than the tuition. I was able to make the Pell grant partially taxable income for the student so that Parent would benefit from the AOTC, The dependent student was below the filing requirement even when making the Pell grant taxable income