I began noticing a bit of watery blood after urinating (sometimes after bowl movements) cytology, cytoscopy, psa, prost exam all neg, except small kidney stone in left kidney, is bleeding normal?

Common: Bleeding in the urine is never normal, but it is common in the context of a kidney stone.

Hematuria: Although blood in the urine is never "normal", there are many possible causes that are relatively benign. Sounds like the lower urinary tract has been adequately evaluated. I would recommend a renal evaluation at this point. A nephrologist would be a good start.