It is not normal as a daily thing. Being a little puppy the vet may have thought it was something minor that the pup was having trouble adjusting to a new food. Something that happens as a daily occurrence over a period of time is not normal. If feeding a small amount of food before bedtime does not help then it needs to be taken up with the vet. The liver should not be over producing bile as a regular thing and bile can be very destructive to the stomach lining over time.
Possibly there is something in the food that does not agree with his particular digestive system but that is only a guess. I'd check the fat level of his food first. Certainly you don't want this to go on over a long period of time.