First time mom peed in nest box

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I recently acquired a mixed breed wooly rabbit from a friend of mine who neglected to brush him, leaving him matted all over. He stayed with his brother (not wooly) who apparently impregnated "him!" What my friend thought were boy parts were mats of hair... So Mama is about 8 months old with 9 healthy babies.
They're 5 days old and I thought everything was going great, but last night she peed in her nest box. I think I've made her nervous by handling them too much, and that it will be a one time thing. But, with all the people mentioning how their first time moms have abandoned or killed their litters, it has me worrying. Right now the only baby that seems neglected is a runt but he's taken goat milk formula through a dropper very well. I also manually feed him by holding mama and putting him on a teat.
I'm just wondering if this event is something that requires immediate action. This is also the first litter that I personally have raised, so any advice on the situation would help a lot!
 
First time moms often just don't get it. Keep an eye on the nest box for more urine and change the materials as needed. If she keeps it up, consider bringing in the box and kits and taking them out twice daily for feeding.

Good luck! And...we like pictures here. :)
 
Everyone is doing well still except for the runt. They're now 8 days old and little Charlie is not taking milk anymore and hasn't gained any weight. At this point I've accepted that he probably won't make it, but is there anything additional I can do? I've grown so fond of this little baby, but he just doesn't seem to have any fight left in him.
 
Most people will probably tell you to help him end his suffering, and I would lean that direction although I know that's a hard thing to do. If you want to intervene you can try to feed him with an eye dropped, and there is a formula you can make on a different thred on here, or the easier way would be to allow him to eat from the Doe first, if he will eat at this point...
 
Thank you for the advice. Despite our efforts, the little runt died tonight. I'm thankful that he was the only one struggling, and I'm excited to watch all the others grow and thrive.
 
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