I'm not an expert, but I know that your puppy's behaviour is an instincitve reaction handed down from his wild ancestors. Puppies in the wild would never be sure where the next meal was coming from, so they would re-ingest their excrement, probably to fill their stomachs, and ensure that any remaining nutrients were extracted. Your puppy will grow out of this habit soon, but you can rest assured, if he is not vomiting, this is doing him no harm.
If you put pinapple chunks in his food ( it has to be wet like ceaser to hide it) then he will dtop eating his own waste. They don't like the taste of pinapple and it comes out just the same way it went in so when he tries to eat it he will be put off by the taste of the pineapple chunks