The same thing just happened to my wife and I. I freaked out for a while, but I've come around to realizing that might have not done anything wrong and we might not ever know what happened... which is definitely scarier and sadder than knowing that it was my fault, but knowing what was wrong.
I'm going to put my science teacher hat on and point out that Ponderosa is probably right. The rat reproductive strategy is to have pretty huge litters. My understanding is that it isn't all that uncommon for a doe to have more pups than they have nipples, which actually isn't all that common in the animal kingdom. When you produce a lot of babies, you're less likely to weed out those kinds of genetic defects, because for the one or two babies that get it badly enough to die young, you might have ten or more babies in the same litter who are just carriers (if they have it at all). Contrast this with humans; if you only have one baby at a time, you're likely to weed out those kinds of kinds of problems. If every baby represents a significant portion of your chance to pass on your genes, if one quarter or one eighth of them get sick, well, you're in trouble and there's a good chance that the negative trait (and your line) will die out in a couple millennia.
This is complicated by the fact that genes are stupid complex, and you get all sorts of weird situations, like a gene that's good for you if you have copy of it but kills you if you have two copies, or something. Again, having few babies tends to simplify this situation; you just can't afford to have too much junk like that in your DNA if each baby represents a significant biological investment.
I doubt that this is terribly comforting, though.
I'm glad your son has the resilience to want to get back on it. Pets like rats are a bittersweet experience - we are so much of our lives, and as much as we love them, they are so little of ours. That makes our responsibility to them even greater, I think, but it also gives us a peculiar relationship.