A contaminated urine sample is extremely common whether you are pregnant or not. In an otherwise healthy person, urine is sterile, so contaminatino by germs suggests that there is an infection of the urinary tract. The problem is, however, that when you wee, the urine passes over your skin, which is not sterile. That is why most doctors will ask for a "mid stream" urine sample - because if you take the urine "mid-wee", so to speak, the area will be rnised and the urine sample will be as clean as possible. However, sometimes, you still get contamination.

It's nowhere as scary as it sounds, and to the best of my knowledge, there are many antibiotics which can be used to treat a UTI, if that is what it really is, that are not harmful to the developing baby.