Hematuria or blood in the urine can be caused by bleeding from anywhere along the urinary tract. The most common cause is an infection because of the inflammation in the urinary tract. Urinary stones can cause abrasion and irritation resulting in hematuria. Other possible cause is a kidney condition called glomerulonephritis. I would suggest that you consult your Doctor so further investigation can be done. You Doctor may request for some blood tests, urinalysis, urine culture, and an ultrasound or CT scan.
In your case, the kidney stones and cystitis need to be evaluated in detail. It is very difficult to precisely confirm a diagnosis without examination and investigations and the answer is based on the medical information provided. For exact diagnosis, you are requested to consult your doctor. I sincerely hope that helps. Take care and please do keep me posted on how you are doing.