My three year old dog had an appointment at the vet today to get a booster shot. Along with the shot is a physical exam. Now I haven't had a problem with this vet before, but I was bothered by what I saw maybe because this was the first time that this happened in the room with me present.
To get samples of urine and fecal matter the plan proposed was to extract via needle from the bladder and then go in and gather a fecal sample.
I stopped them and ended the visit after they tried to get a urine sample and did not. I am just so bothered that I even let them try it. Is this a normal test? Why hasn't this come up before? It seems much too invasive for a healthy dog.

How wise you were to stop this vet from caarying out a totally unnecessary invasive procedure. I have never heard of this being done as part of a routine vaccination

How old is your pet? Once a dog reaches 7 years old, yearly bloodwork and urinalysis is highly recommended.
What you witnessed is known as a cystocentisis and the reason they extract the urine in that way is so the bacteria in the lower urinary tract does not contaminate the urine.