The nursing pups can have contamination from each sharing all of the nipples. I was told to wait 3 hours and that they cannot be sucking on each other during that time.
Adults should not eat 2-3 hours before swabbing because of the food contamination and should not be sharing a water bowl. I usually crate them for a couple of hours before I swab.
I have been the collector for a number of DNA clinics with our local show circuit. Because you never know when the dog last ate, drank, licked or otherwise shared body fluids with another dog, you have to collect in a way that avoids contaminated results. I use a spray bottle of distilled water to rinse out the cheek pouch, then wipe it with a fresh paper towel before collecting the cheek cells with a swab. We have never had a problem sample