The fry won't have been a neon tetra; they're actually very hard to breed and the eggs won't hatch in a normal community tank, even if they spawned in there.
I can't imagine a neon being big enough to eat a molly fry. If they have been eaten it was probably the mother, unless you have any other kinds of fish in the tank. Livebearer mothers often eat their own fry; I've seen one turn around and eat a fry literally moments after it was born. They're not that bright, and don't recognise their own offspring.
She'll probably have more, anyway. Most livebearers, including mollies, can store packets of sperm, so they can continue getting pregnant, even if there are no males present.