I think you don't panic, you make changes all the time and your mother rabbit gets stressed. It is very hard to advise as it is not clear without photos. I understand she lives in a 100 cm cage with her 2 babies from her previous litter 1 month ago and you removed older babies to stay somewhere else?i removed the babies as soon as i saw that the mom gave birth.
One little one looks like he has blood on him. Im not sure what it is! S/he is sticking to things cuz of the blood or whatever it is. Is this dangerous? There is fur that got stuck and also the blanket i put in the nest box! How do i remove it from s/he?
The mom has messed up the next box! she dumped all the contents onto the bottom of the cage! Why is she doing this?? Im going to put everything back in. Please help!