Sorry to hear about the snake. There's a pretty large array of things that could have happened. You might already know a lot of this, I tried to be thorough. I also tried to rank them in order of likelihood, but other may have different opinions.

 1. Shedding complications - You didn't mention anything about shedding, but stuck sheds can be very dangerous for young snakes especially. Any stuck sheds should be dealt with promptly. Additionally, shedding in patches is a sign of illness. 
 2. Illness/infection - It's entirely possible that the snake was sick or got an infection. Something like snake mites that's less serious for an adult snake could pose elevated risk to young ones. If you haven't already, i recommend removing the live snake, and completely disinfecting their enclosure.
 3. Improper environment - While corn snakes aren't too particular about their environmental needs, babies are more susceptible to lapses in husbandry. Heat in particular is important for digestion. Apologies if this sounds accusatory, but it's worth mentioning.
 4. Genetic defects - If you got the snakes from a pet store or mass breeder, they could have had some genetic defects that were completely out of your control. 
 5. Food poisoning - While not very common, it's possible that the pinkies you used were contaminated. Most of the time, the prepackaged ones are safe, and the fact that the other snake is still alive suggests this isn't it, but it's still a small possibility. 

    Unfortunately, the only way to know for sure would be to shell out some money for some tests. I would just keep a close eye on the remaining snake to see if you spot anything out of the ordinary.