Have you been feeding more heavily because of the fry perhaps?
What were the numbers for pH and GH? I don't believe they were the cause of the issue here, but any numbers for those are fine, it's whether they're suitable for a very hardwater fish like mollies in the longer term really, she might be more susceptable if your water is on the softer side.
She also looks as though she has white stringy poop - have you ever wormed your fish? Did you buy them from a big chain fish store or a local, privately owned fish store?
Addition since new comment: please check the exact temp on your tank and let us know.
But the ammonia and nitrite spike are the biggest concerns and likely cause of the current problems. Why the ammonia spiked is a concern, perhaps over feeding, but a dead fish, snail or shrimp can cause the same thing, so checking carefully for anything like that is important.
As
@AilyNC said, it's vital to keep ammonia and nitrites at zero. Ammonia is highly toxic to fish, it literally burns their gills and skin, and nitrites block the bloods ability to carry oxygen, so also incredible damaging to them and both are eventually fatal. So keep doing large water changes to dilute it out until ammonia and nitrite are staying at zero again, and nitrates stay low.
Did you do anything with your filter? If you washed it in tap water, or replaced cartridges, that could have lost a lot of beneficial bacteria and caused an ammonia spike.
