Our puppy is nipping my son. why?

We have a 5 month old mixed breed 25 lb puppy that nips one of my children (12 yr old boy) The dog is is well behaved and easily getting trained in all other areas. My son (we have 3 children) was not home when we first got the dog, came home from summer camp 2 weeks later. I think the dog sees him as an outsider and a threat and therefore nips him. This has been going on for a month and I am getting very concerned. We are working with a trainer (that I like) but she does not think my theory about this issue is correct. She suggests that we immediately get the dog to lie down and hold him there and otherwise ignore him when this behavior occurs. However, the behavior is persisting. Please help with any suggestions.