Fry Dying

was the male still kept in?
what about your water chemistry?
how deep is your spawning tank?

male was kept in the first time for 4 days. Second time he was not interested in the nest after a couple of days and i took him out. Many eggs fell to the floor before hatching. The tank is about 5 inches deep. Maybe i am not turning on the filter soon enough? When then? I didn't test the water. One person suggested to leave the fry alone for the first week. I will be making another attempt next week. Any suggestions would be helpful.

It's definitely not a filter problem.
What it can be are 2/3 possible things:
1) water chemistry. Adult bettas can tolerate a plethora of conditions where as the fry/eggs cannot. With certain species of fish, hard water stunts fry development or even fertilization all together.
2) male behavior-- some bettas aren't meant to be fathers.
3) improper conditioning. Male is too fatigued to tend to the nest.

first time i used r/o water. Second time i used tap water with conditioner. So softer water would be better? I was also conerned about the amount of debris on the bottom of the tank in just a few days, too many plants floating at top? They hatched on time but never got past the yo-yo phase.

that shouldnt be a problem. quite strange indeed--from what you are telling me, it seems that everything should have worked out. didnt you remove the male a bit early the first time around? try using RO water and remove the male a bit later, 72 hours from hatching.

also, it is normal for the nest to deteriorate significantly after hatching--it does not mean that the male is not tending to the fry. rather he's spending most of his time catching them and shoving them up into the nest with a makeshift spit. keep the tank well covered and protected from drafts to help extend the life of the nest.