why did you wait until the very end of your time period to get the certification done and honestly why did you expect a Minute Clinic doctor to be able to do it? Did you ask them when you made the appointment if they were familiar with the process/form? A quick Google shows me a bunch of bad reviews for DOT physicals at Minute Clinic. Many are that while they are on the approved list, they don't generally do them often enough to be familiar with the process.

If in the end you got what you needed and weren't required to pay any extra, I don't see where there is much you can do except write a bad review.