Chances are, they weren't allergic. It was probably just an excuse. Perhaps a puppy was more work than they realized. So, let's say they had called you and said, "I'm sorry, I think we bit off more than we could chew. Can we return the puppy? She's just too much work for us." A good breeder should take it back no matter, simply for the fact that they don't want their puppy in a home it's not wanted. Because if they don't want it, eventually, they'll give it away or take it to the pound. Very sad, but true.
But many breeders out there would just say, sorry, no returns. So many people will claim allergies for an excuse. The truth is, it is best that she contacted you, whether or not she was lying about the allergy, so you can decide what happens to your puppy.
You did the right thing.