I've had squabs murdered. Couldn't find the culprit, but had my assumptions. But I have a loft full of several pairs. My first thought for the OP was to wonder whether perhaps the hen had these babies out of wedlock (fooled around with another cock bird), in which case the husband cock might try to kill the squabs, but it sounds like you just have this pair, so I am as perplexed as others.
Were these her first found of youngsters? While it should be genetically wired into her to know that her cock bird should share the duties of caring for squabs, it appears maybe it is not, or maybe he did something she did not like. I would closely watch them. If this continues, I would not let this pair breed again. If it happens more if and when you try to breed her to other cocks, I would not breed her at all anymore.
Whether pigeons are bred for speed, looks, temperament, etc, IMO good parenting genes and skills should always be a factor in deciding which birds to breed.