At first, the young mammal is aided by his mother's milk. Milk changes composition throughout the day and night and is thought to help entrain the young mammal to changes in light for sleep/wake cycles.
But after weaning the young mammal is again at a fork in the road with circadian rhythms and now must stand on his own with sleep/wake cycles.
So, it's not surprising that young puppies show short sleep cycles and wake up seemingly randomly. Their endocrine systems are still developing the internal clock needed to regulate sleep-wake cycles.
It's also not surprising that we see most of the breeders complain about 4 AM screamers in that 5-6 week old range - probably just post weaning for many breeds.