They are adorable! I have a Kaos too. :-) Anyway, I would separate them in two separate crates immediately. You have to be VERY careful with litter mates as they will bond to each other and not to you if not treated separate. My Kaos and Nala are litter mates and we have been fortunate to avoid all problems associated with litter mate syndrome but we worked hard at it. They pups are always crated separately (apart from the first few nights at home with us), at the beginning even in different rooms. We would feed them separate, take turns with different combinations of dogs (we have 3 total). My vet felt so strongly about litter mate syndrome and avoiding it that he wouldn't even see the pups at the say time during those early shot visits. He had a bad experience with litter mates previously and was worried when we adopted Kaos and Nala together. You can start with crating them separate but so they can see each other. That may help ease some of the inevitable crying for the first few nights but I would start sooner rather than later.
As for the poop problem, I would run them both to the vet to rule out illness first and foremost. Once they have a clean bill of health, it could be any number of things. It could be stress, an allergy, something they got into that they shouldn't have, etc...once you have them in separate crates it will be easier to figure out who is having the problem and why. Like I said in another post, I won't lie and say separating them is going to be easy. Those first few nights are going to be awful; however, you HAVE to stick with it. Giving in when they cry is only teaching them that crying and whining will get them their way and make it much harder for you in the long run. It should only take a few days and they will settle down but it is tough until they do but some rough nights now may save you years of difficulties and heartache down the road.
Good luck and keep us posted how they're doing!