First, what kind of puppy do you have? If it's a german shepard, I can give you a really good guess at what it probably is...persistant aortic arch. It's hard to explain what it is, but it can be diagnosed by a vet with a thorough work up.
Other thoughts are strictures of where the esophagus meets the stomach, or else a condition called megaesophagus, where there is a pouch off of the esophagus that traps food. You will need to go to a vet to diagnose either of these conditions.