Causes include lesions of the urinary tract, contamination during menstruation, 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. My sincere advice would be to consult a urologist.
I hope that helps. Take care and please do keep me posted on how you are doing or if you have any additional doubts. Kind regards.