Sometimes people wait too long before going to the toilet and then don't fully empty their bladder (which should happen) when they do go to the toilet. I saw this once on a medical documentary when a girl had a fear of toilets, although it's not necessarily caused by that!
Also, maybe the infection had cleared by the time the doctor did the test. Often in adults the problem can clear in 24-48 hrs.
Could also try encouraging her to drink plenty of water, a glass of cranberry juice a day, not anything too sugary/acidic, cotton pants (as opposed to synthetic), that kind of thing, the same you would for an adult. Obviously keep monitoring her too and maybe badger the doctor more!
This might help..
http://www.nhs.uk/Conditions/Urinary-tract-inf ection-children/Pages/Prevention.aspx?url=Page s/what-is-it.aspx
Hope she gets it sorted