Washing the car the other day i noticed a couple of small bubbles just above the rear number plate in the recess.

There are 3 small bubbles in total but 1 is seperate to the other 2 but the biggest is probably about the size of a 5p coin.

What is the situation regarding the warranty and bodywork?

If rusted through from rear of panel it's a warranty issue (10 years perforation warranty). If a paint defect it's out of warranty as paint is 3 years warranty. If caused by wear and tare non warranty in either case.