When the fry become free-swimming, they need to eat tiny foods. That's the time when most fry die. If there's a lot of fungus in the tank from dead or infertile eggs, then it can also kill the fry. Methylene blue can be added to the water to kill fungus but the fry (and all fish) are sensitive to that so it's only for the egg stage (a day or two when the eggs are first laid).
Yes, eggs or fry that die can actually vanish within a day as fungus, bacteria, and microorganisms can eat them up that fast. If they were in a solid breeder trap (no water flow with the main tank), then the water quality would certainly be worse in there. Some egg could rot but that alone shouldn't have killed them. Fry are very sensitive. I've raised many fry but even I have a high mortality rate. I have never raised goldfish fry indoors though (just in my ponds).
Oh, you say they were swimming vertically. That's normally how fry behave for the first few days. They are not yet "free-swimming" but living off of their yolks for a few days. Once at the surface, they are free-swimming and need to eat. I now read that indeed you had a hard plastic type breeding trap with slits. You bet that fry can go right through those if the trap is not solid all over. You need a net breeder instead or put the fry in another tank or a pond. You could also cover the entire trap with pantyhose. The thing with net breeders that I've found is when I go to clean them out with water changes, I often accidently squish or hurt fry. For that reason, a separate tank is generally safer but more work.
Your temperature is fine and some sunlight can actually be good as it makes algae and microorganisms grow which the fry can eat.
My page on breeding is at
http://www.fishpondinfo.com/breed.htmBetter luck next time!