TURBT, blood clots, blood thinners

I had the TURBT procedure about three weeks ago, discharged with a catheter. The day before my follow up, I had severe upper back pain with shortness of breath and had to be taken to the ER. I was diagnosed with blood clots in my lungs, put on a blood thinner and kept overnight. There was a problem with my prescription when I was released so I was without blood thinner medication for two days. Once I began to take the medication, my urine turned very dark with small coffee ground-like granules that settled to the bottom of my catheter bag. Has anyone experienced this situation? My follow up with the surgeon is scheduled for early next week and hopefully the catheter will be removed, but I am wondering if I should be concerned enough to go ahead and notify my doctor.