Just like us humans, dogs do not like every dog they meet. Especially in tight spaces it can get a bit growly at times, so I always look for enough space for all dogs involved to move freely and express their body language. Being and staying calm yourself will also help a lot.
Could be many things in the stomach-intestinal tract, I guess. When our 2 B's were on kibble they farted a lot. Our then vet said that was because 'they are meat eaters' - we found that a funny explanation as they were not eating meat then. Later we switched their diet to 100% fresh meat and the farting stopped within days. If you go on Amazon you can find lots of probiotics for dogs with reviews. All in all I think meat is better for dogs, also for other reasons.
We don't use a crate ever. Be sure to train your dog to be alone step by step, leaving her only a minute at first, then building it up to longer periods. What also helps greatly, strangely enough (or not, dependin on your view of dog intelligence): tell her that you will be out for a while, AND when you will be back. And then make sure you are back at that time. We find them sleeping in the same position even after hours.
And during puberty, a few months on, you might experience another kind of nipping. Now it is playing, then it will be a test of your position of leader of the household. Same thing: keep calm and in contact and let him know with words, energy and consistent body language that you are his loving 'boss'. Depends greatly on the individual also.