Sometimes that happens, it's happened to me too but I'm very blessed to have met someone very well educated who has clarified some of my doubts.
But in general, if you're having doubts in my opinion I always think back to the fact that (ATLEAST TO ME) it is clear that a creator exists - even though people may disagree. This being must be all knowing since there looks as if there is intelligence in design and in terms of law. Therefore when looking at these doubts and issues, just because it seems irrational to me that a loving God would allow these things to happen that doesn't mean he doesn't exist. By nature I am limited in my rationality and intelligence, therefore how can I expect God's rationality to match with mine. If God exists then there is a possibility of a greater plan behind this and if so, we have drawn the short straw if children born with such horrific illnesses are guaranteed heaven when I am not.
I know and agree that some of these things are just sad but I try to humble myself because I know I am limited like all humans and maybe there's things I just wont understand. But what I find worse is that whether an innocent child dies or a murderer dies, from an atheistic point of view what happens after they die is irrelevant since there is no afterlife. So what is the point of being good, maybe it may help society for a mere few years but out of the 14 billion years of the universe's existence, technically your good actions are insignificant- unless God exists. It's sad to think at the end of the day, looking at the wider perspective what you do in life is irrelevant, your existence is a mere pixel in terms of the life of the universe.