Sounds exactly like my dog was. Seems you aren't "pack leader" yet. Despite success in training right after rescuing, my dog did the growl/nip/bite when scared thing for months after. Maybe 6 months in he actually tried to bite my hand for real so I lifted him off the ground and flipped him over on his back and pinned him with both hands - got loud so he knew I was not playing and stared at him making sure he couldn't look away from me. He retreated from me for a few hours after he relented and I let him go, tail between his legs, but he's now a fantastic dog. The worst he will do is whimper when he's scared instead of growling. I was afraid we'd have to put him down (I can't own a dog that I can't trust not to attack people) but he really responded well and even started trusting me more and wants me to play catch with him where before he would run away with toys afraid I would take them. Now he knows I will so he's OK with sharing and playing fetch since it's really "my" toy in his eyes. When he does something bad and I call him out on it instead of hiding, he will slowly walk over with his tail between his leg and I will scold him verbally and he looks away. I just treat him passively for a little while then we go back to normal. He doesn't really have many accidents but I never punish him for reasonable ones (like when he's sick or we were gone for 12 hours) - he will still show deference when I go to clean up the mess but I just pretty much ignore reacting to it otherwise and he is fine right after.