I have guppies (which means I have fry), and strangely have a similar issue.
There's probably a certain amount of cannibalism, but it's also worth looking at your filter intake. I have enclosed mine with a fine net, so the small fish don't get sucked into the filter (& I guess they wouldn't be saying 'wow... what a ride' !!). A separate tank is clearly the best way to go, but 'mum' wouldn't say no to a bit more live nutrition, so get a breeding trap too for maximum survival.