It is unlikely that your symptoms were due to pyelonephritis (kidney infection) because they resolved before you started antibiotics. Your sample may have been contaminated because it sat around for a few hours before i was tested, or you can have a contaminated sample just from bacteria on your skin. It is difficult for me to tell you to stop a course of antibiotics once you have already started (and a repeat sample won't be reliable now that you have been on antibiotics), but I agree that the cause of your back pain was probably from something else (possibly muscular) if you had no other sympoms of infecion (fever, chills, nausea, burning with urination, urinary urgency etc).
If you have almost finished the prescription, I would just finish it (if you are not allergic, there is little harm, as side effects are rare), but stopping it is a reasonable option considering the situation. If you do, make sure to be reassessed if your symptoms recur.
JMK MD
I am taking Cipro 500mg twice daily.