Hi there, I brought little Bambi home Saturday, and she has done great with us and our pets and the move. (Moving from her home to ours

) She got her 2nd set of shots on Tuesday. Oh my word, the worst experience of my life, she yelped so loud and continued crying for a moment, which I have experienced with other puppies and kittens, but not a little bitty yorkie.
That night, my boyfriend and I were lounging on the couch with her, and he gently picked her up (she was dozing) and she yelped like he had stepped on her. We weren't sure exactly what had happened, but came to the conclusion that he might have hit where the shot had been given (rump). A couple minutes later he picked her up again and she whimpered, not as loud.
The next night, I grabbed her to rearrange her and she yelped again and curled up towards my belly away from me like she was trying to hide, only this time I had been diligent not to touch her rear and had picked her up by her middle.
My question is, has anyone experienced a yorkie startling quite so severely? Possibly from a nap? That is my second theory. Possibly she was just sleeping and we scared her, although I have never heard of that before. We have felt this puppy up and down without a sound, no bones are mishapen and she doesn't seem to mind. I'm going to ask the vet when I see him in a couple of days, but I feel like the answer I will get is "It's probably nothing" after they examine her and she doesn't yelp.