You shouldn't have to worry about getting flamed here. You did try
to keep Angel chaste, she was just a very naughty devil of a kitty!
I've only had one litter of kittens born in my bathroom, two orphaned litters at 9dys old and about 2-3wks old, the rest were trapped ferals around weaning age.
I foster, TNR and rescue a little.
Anyhow, the litter Shadow had stayed in a cat carrier and they didn't try to get out. From what you are describing, the black kitten is just more mobile and it seems like she is trying to encourage it to be still. Can you isolate Angel and her litter in a smallish, quiet room? Shadow was kept in my larger master bathroom. You could do the same if it isn't an often used bathroom, or keep her in a room with maybe one or two suitable kitten nesting sites. When I tried to leave my bathroom door open for Shadow to have more room to exercise into the master bedroom, she tried to move the kittens under my King size bed. I couldn't have them under there on the carpet so I got them out and had to keep her in the bathroom and let her into the bedroom only when I was there to make sure she didn't try to move them.
Mother cats often bite the necks of their kittens, especially when grooming, and it does seem like the equivalent of a human mother saying "Sit still until I'm done with you!". I think I'd just keep an eye on her and that kitten, but because that kitten is the most active, that may be the only reason you are seeing her do this with this particular kitten, especially if it appears healthy in all other ways. I suppose you could bring her and the litter to the vet for an exam to rule out a problem with the black kitten, in case she is thinking she needs to cull or reject it, for whatever reason...but if my finances were tight, I think I would save my money for vaccinations and spaying.
Anyhow, welcome and good luck!
Oh, PS... any pictures you could post? We love seeing kittens!