Causes include lesions of the urinary tract, disease of the prostate, trauma, tumors, malaria or stones
in the urinary tract. In your case as kidney stones
are present, so these definitely need evaluation as nephrolithiasis or kidney stones are known to cause hematuria. Moreover it can cause further complications. My sincere advice would be to consult a urologist.
I hope that helps. Please do keep me posted. Kind regards.