It sounds as though you may be looking for a tactful way to handle this situation. How about pleasantly telling the nurse, "Oops! Someone forgot to change the pillow cover." -or- "Doctor, you need to get a clean probe."
If said respectfully with a smile I can't imagine anyone taking offense at this unless they're deliberately trying to save a few pennies at your family's expense. In that case you need to find a new doctor. Always keep in mind that YOU are your and your son's first line of defense.
Whatever you do, don't allow the exam to proceed until they've made the needed corrections. Remember, they work for you and need to earn your business.
I don't know about the laws in Florida but having an unsanitary exam room is not only unhealthy I bet it's also illegal.
Until later...
FT