Maybe he/she is very uncomfortable with you touching him/her. Try to create a bond. Give her/him dog treats. Hopefuly he/she will open up to you. :)
Perhaps he's trying to exert some dominance? He's a growing pup and sometimes at that age they're becoming more aware of their personal space. He might actually feel a little threatened by you. If you're stroking him while he's eating, you need to stop doing that otherwise he'll think you're tying to steal his food from him. If he growls while he's playing with a chew toy (I assume he's teething now?), he's just being playful but you need to be careful here also otherwise he may get into the habbit of being a little aggressive. Just remember that you're the boss and he depends on you. Be fair, but assertive with him (or her). Hope this helps!