Dog attacks puppy when growls?

I have a female dog. Just got a new puppy. When I'm playing tug of war with the puppy and he growls she attacks him. Other times she is staring him down or smelling his private area. Then at times she ignores him. The puppy also will run up and play and bite her and she will run from him. The puppy is always happy to play around her (tail wagging constant). So why does she attack him at that point and smell him alll the time. We've had the puppy for a few weeks