There could be lots of reasons for them doing this.
Some things that should help...
Sometimes kitties get very finicky about exactly how their litterbox is set up, and where. Sounds like that's the problem here.
Our boy, Hobbes, did the same thing, and it turned out he wanted one litterbox to poop in and one to pee in, he didn't like hooded litterboxes, and he liked it pristinely clean. I found a couple websites that helped me understand exactly what it was that I could try that would help, and it really did. One good thing is the fact that he's now outgrown his pickiness about wanting two and wanting them in such perfect condition, now that he's about two! Hopefully yours will do the same!
Here are a couple websites that should help:http://www.larimerhumane.org/services/litterboxinfo.cfmhttp://www.thepetprofessor.com/secA...es_and_cats.asphttp://www.heartlandhumane.org/pub/petcare_litterbox
A couple tips:
Cats don't usually like the plastic liners some people use in litterboxes.
Some cats don't like the hooded boxes.
Cats at times don't like the box to be anywhere that they also have to eat and drink.
Sometimes the problem is just that the box isn't somewhere private enough. They only like to "go" somewhere that is low-traffic, quiet, and very private.
Also, try putting the litterbox in the place that he's been pooping so he gets the idea. Also be sure to put the poop that didn't make it in the litterbox, so he gets the reminder.
It sounds like your babes don't use a litterbox...could one of them be asking to use one?
Hope all that helps!
Let us know how it goes!