Should I ~ OR ~ Should I not ... politely dispute a charge on a bill I received today for my dog's urine ... ?

If I were in your position, I would point out that she was only to be there for collection of a clean sample and that she had just recieved a full physical, so this cursory physical was unnecessary. Some vet places will be happy to refund that portion of the bill, but others that are run by corporations won't be so ready to do so.