The ammonia is a combination of a new tank with no developed biological filtration, poop on the bottom, uneaten/dead food, egg casings from hatched bbs and/or unhatched bbs eggs that are rotting in the tank if any were accidentally put in the tank when siphoning bbs from the hatching vessel for feeding. All of that combined will, believe it or not, deteriorate water quality quickly in a tank with no established biological filtration. Which is why it is imperative to keep the tank spotless.
During the first week, I siphon my fry tank 3 times a day. Yes, I have to wake up a half hour early. Yes, I do it as soon as I get home from my 12-14 hour day...even though all I want to do is sit on my butt and relax. Yes, I do it again right before lights out at night. Then I start all over again the next morning. Trust me, I have siphoned a fair amount of fry out of the tank. I just take them back out of the bucket and put 'em back in the tank. No matter how careful you are, at some point, you'll suck of of the fry up so don't get too upset or let it stop you from keeping the tank immaculately clean.
I have on more than one occassion, as have many who are raising fry, used Amquel and/or Amquel+ in a fry tank to help with ammonia issues with no negative effects. An indication of high ammonia in the tank would be the fry scratching their heads or flipping their tails up to their gills. If that is happening, you need to remedy the situation ASAP.
As I've stated on this site and others, I use large Hydro sponge filters in my fry tanks & juvie tanks. They are awesome filters and provide more than adequate biological filtration. I would get a sponge filter in the tank ASAP so it can start to colonize beneficial bacteria. Until then, you may have to do massive daily water changes, as you're finding out.
As difficult, time consuming, semi-costly, stressful, frustrating as it is trying to raise fry - I would not trade the experience for anything. It took MANY lost broods of fry to find a system that worked for me. Even now, it is not easy - but it IS easier than when I was struggling to find something that worked. Never give up, use any failures as a learning tool to "tweak" your system for the next time. You will find a way to do things that fits well with lifestyle and time you have available.
Best of luck!
Tom