There's a size limit to each herd, so a beefalo won't make babies if their herd is at capacity. Maybe your "captive" beefalo are still considered part of their original herd? Try letting one out and see if it walks home.. if it goes back to a big herd you've found your problem.
I've got the same problem as the original post.. My domesticated, bell bonded beefalo keeps spawning babies at my base. EVERY year there's a few new babies, and I hate having to kill them. Who is she mating with anyways? Does anyone know of a way to keep your beefalo from making children? Klei needs to make a Beefalo contraceptive pill,, maybe a Beefy IUD?