I'm sorry to hear about your loss. It's always hard to lose an animal. It's not uncommon that by the time an animal shows any physical signs of an infection that it has progressed considerably - they're very good at hiding signs of illness.
In truth, the answers you're looking for would be better off being answered by a vet if you really want to know what happened. The best we will be able to do is speculate, and that isn't likely to provide you with any real answers. If you decide to go that route, make sure your little one is kept cool (NOT frozen) and then make an appointment with your vet for a necropsy.
Again, I'm sorry to hear about your baby. It's obvious you cared for her a great deal.