Please understand I am just saying this as we had a similar exp. w/ a Mother (beagle) who would constantly push this certain little one, who was also the runt, away and out of the whelping box. She started doing this day 1. I had to nurse this little guy, whom I named Leppy for 2 weeks. Poor Little Leppy didn't make it.

It was as if the Mother knew he wasn't well and didn't want him around the rest of the litter (of 9 pups) But I see you said it happened to 2 diff pups, from what I understood. Maybe and praying it is a whole diff reason of her doing this then what we had, but I just wanted to share a similar exp
Do you have any pics up of Skittles new family?!?! I would love to see them