Hi!
What a cool thing you've got going on. Colony rabbit raising is such a humane, sweet and kind thing. Lucky babies!
I know that sometimes when a mother rabbit is nursing her kits, she will get out of the nesting box or area rather quickly and some kits can get dragged out - if they are really new to the planet, and without their fur, they can freeze to death at night and then you will find some casualties outside of the nest box - usually just a single kit.
What we did was make nesting boxes that had a V shape cut into the opening - this acts as a catch when a kit is still hanging on to nurse and mama jumps out, the V shape effectively stops them from being pulled out of the nest, as it "scrapes" them off the teat and deposits them back in the nest.
We made the nesting boxes to look just like a cube - covered on all sides with the entrance side cut in a V shape just big
enough for mama to hop out. Once we did this, we never lost another baby.
Now, if the baby has trauma (blood, broken limbs, feet eaten off) then it's being attacked by one of the does. Simple solution of just separating the mama's for a little bit. But it doesn't sound like trauma.
Anyhow - hope that helps. I'm sorry about the dead babies. That's never a good thing to come out and find.