Never leave any puppy under 4 months of age alone with an adult dog. Always supervise them when they are together. Puppies don't yet have enough development of dog social skills to properly respond to an adult dog. They can deliver a huge insult, not respond properly when the adult takes offense, and it is entirely possible for that pup to wind up hurt or dead.
Your pups need time apart from each other, too. It is important for their proper development and bonding with humans, and also so that whenever they are separated in the future, they will be able to handle that without pining and maybe starving or getting sick.
You didn't say whether the Border Collie injured either of the puppies. Sometimes what looks like a fight is not a fight. But to start with, I would have him with just one puppy at a time and under your close, close, close supervision.
Puppies need a lot of rest anyway, and they need to get used to get spending reasonable periods of time in a crate. This is the time in their lives when it will be easiest for them to develop this ability that at some point might be a life saver for them. Separate crates--do not put two dogs in the same crate.
I have written some articles at the link with my signature that will help you. One in particular for you to read is "Two Puppies or One?" The titles are in alphabetical order, so just scroll down to it.
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Kathy Diamond Davis, author, "Therapy Dogs: Training Your Dog to Reach Others," 2nd edition, and the free Canine Behavior Series articles at http://www.veterinarypartner.com/Content.plx?P=SRC&S=1&SourceID=47