Talk to the fish people at the pet store for advice, they are usually pretty helpful. Personally, I would either buy one of the small isolation tanks that hangs inside of your regular tank, or buy one of the partitions they sell that you can use to divide off some portion of your tank. Either way, it should give the babies a little time to grow before venturing out. My best guess is that either the big fish are injuring or trying to eat them, or, they are simply not strong enough yet not to get sucked into the filter. Good luck.
It's likely that the bigger fish are killing the smaller fish - rule of thumb is to keep all the fish a similar size in the tank. Look out for chasing during the day - in the quiet of the night killing may happen.
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