Do you have wire on the bottom? I'd probably cover it and put down an inch or so of pine shavings. Is it in a cold area? You may want to keep it in a heated area. I've lost a few mouse and ASF babies from cannibalism, never had rats just ignore their young. I never bred in a group either, maybe that with new moms could be the issue. Seems like the new moms have the most trouble until they figure out what is going on.