Many tests will be done with a split specimen. They will make you void into the initial cup with a temperature strip, then they disburse the urine into the two vials for the lab. Some labs test the first vial and they store the second vial for further testing if necessary. This is needed when there is a dispute or if they spill or drop the first vial.
If the collector checked the box indicating that the temperature was in the correct range, you should be fine.