Sweet little Winnie!!

Hi everyone! I'm new here, but my mom told me about this site, so i thought i'd give it a try!
Anywho, I'm INCREDIBLY upset over an incident that just happened about an hour ago! Basically this is the whole story:
We just took in a cat named Eleanor Rigby about 4 months ago. And she use to be an outside cat but we converted her. But she accidentally got pregnant, at the age of approximately 9 months old, and just gave birth to 5 beautiful kittens last Saturday. Tomorrow they will officially be 1 week old!! :D But today, the second smallest kitten, Winnie, just opened it's eyes for the first time! We were completely in awe! And our momma cat is a total sweetheart and trusts me alot, so she lets me near her & her kittens 24/7. I was shocked when i saw Eleanor carrying poor Winnie by the scruff into my room ( she's staying in my mom's room )! I went to go inspect what was going on, and i found Eleanor, guarding Winnie between her paws under my bed! I began crying because i was scared for poor Winnie. But i took action and safely carried Winnie back to her litter mates where Eleanor followed, and soon let Winnie nurse till she fell asleep. I want to know some reasons why Eleanor would have seperated Winnie, but yet still want to be with him/her!! It's not like she just abandoned Winnie, just kept her away from the rest of her litter. Some of my sources tell me it may be beecause she does not know if Winnie is healthy becasue of the sudden eye opening, or because she is stressed and picked Winnie to help her out with some alone time...I'm not sure!! But i am willing to expect the owrst, because my mom does NOT have the kind of money to take the kittens to a vet right now! And I think it was a sudden thing, not like she was rejecting Winnie.
Please help me out!!! :(

xoxoxo,
Alexa <3