Hi and Welcome to YT!
Yes, it's very common in small dogs, and to prevent it from occuring, many vets give the DHPP at one visit and the Rabies 3-4 weeks later. Surprises me that he didn't do it this way to begin with, knowing it is common in small dogs.
See the YT Library:
http://www.yorkietalk.com/forums/yor...-overview.html
You'll find some more vaccine related articles there too.
She may now have reactions in the future, so I would find a vet willing to do a minimal vaccine protocol with her to be on the safe side.
How old is Ella?