Why did zebra danio die?

I recently started up a 3gal fish tank. I have it fully set up with a heater, Filter and air stone. I let it run a few days in advance to let it start cycling then added some hardy zebra danios(4) i really should of only used three because of the 1" to 1 gallon rule but i needed to have a school of at least 4 so i didn't think it would be to bad. i use Tetra chemicals Aquasafe,Easybalance but now two weeks later one of them was upside down of the bottom of the tank no injury of sign of indifference from the others who all were active and happy. I think it might just be the tank's natural cycle that caused this but i am unsure. can anyone add any insight also i did a 1/4 water change and added more safestart.