I am not sure that the dark blood really has anything to do with the medication. I'm guessing (not a dr.), that the darker blood is old blood & since you're only spotting now it would seem normal. I've had 4 d&c's and I have never had an infection either. My dr always prescribes anitbiotics after my procedures. The symptoms that you described sounded more like a urinary tract infection to me. Those are miserable!!! Feels like you need to REALLY need to pee, then when you get in there, just a few drops will come out & it burns. If you are concerned or not feeling better, I would definitely go back to the dr.
It's really hard to say based on the info here. Yes, spotting off and on after a miscarriage and a d&c is pretty normal. It takes time for your body to get back to normal, and as long as the bleeding is minimal (no more then a regular period) it's no big deal. If the bleeding gets heavy, or starts to be accompanied by clots, you do need to seek emergency medical treatment as it can mean that something was missed in the d&c.
The bacterial infection bothers me. I have had to have 3 d&c's and that has never happened to me. I would follow it up for sure, and given that your Dr's attitude is that "it's probably a bacterial infection", I might see another Dr. That has the potential to cause problems down the road, so please make sure you are staying on top of it.
I'm sorry you had to go through this, and I wish you peace and healing.