It is not likely to be due vaccination, however all things are possible in nature. More likely is that stress of vaccination set your puppy up for another type of mild infection/fever. This, coupled with a visit to a clinic where sick animals also visit (and therby provide plenty of microbial challenge) can cause puppy/kitten illness a few days after vaccination.
Ever notice that pediatricians' offices frequently have a sick waiting area and a well waiting area? It is to minimize transfer of sickness among children. I wish we as veterinarians would do this, too, with our healthy and ill patients.
Perhaps a telephone consult with your vet will allow a plan of treatment so that you don't needlessly expose your puppy to more challenages.
Dr. Van Lienden
Dr. Raymond Van Lienden DVM
The Animal Clinic of Clifton
12702 Chapel Road, Clifton
Virginia, U.S.A. 20124