Garlic Help

I have a garlic garden of 350 bulbs. I have noticed (and removed) 6 bulbs that were much smaller than the rest, had more brown leaves than the rest of the crop and seemed flimsy. Upon pulling them, I discovered that they came out easily, were small bulbs, and seemed to have a bit of rot. I live in New England (zone 5) and I think I am 2 weeks from harvest time. Also, I pulled one of the healthy looking plants, and it was perfect looking.  My questions are: can anyone help me identify the rot? And, is the rest of my crop doomed? I read a bit, and it seems that some rot can continue  to develop post harvest. Help Wanted!!