Danios are egg scatterers. They swim quickly up and down the length of a tank and scatter eggs along the way. The males will be chasing the females and dropping sperm. Eggs that manage to fall into places like between pieces of gravel will not be found right away and eaten. Those eggs will be the ones that hatch and provide those extremely small fry that you are finding.
O,ok, so really there would be no use putting a female Danio into a breeder since they need room to swim and drop their eggs. So the only way to keep the fry safe in this case is to wait until I can see them and then put them into a breeding net right?
Also, should I not vacuum the gravel for awhile in fears of sucking up some of the egss or doesn't that matter? would those eggs maybe not be fertile?