My daughter has had cystitis, for which she has taken over-the-counter medicines. last weekend she was complaining of pain in her kidney area, but by?

Pyelonephritis?: Urinary tract infections that reach the kidney(s) is called pyelonephritis. While she could have other causes for "kidney pain" (such as a kidney stone, diverticulitis, ....), i would be concerned about her having a kidney infection. Regardless, she should probsbly be further evaluated (repeat ua, renal us, possible ct ivp, VCUG ( to r/o reflux, ...).