No. It could happen at any time. During the night, they're sleeping. Pigeons don't fly around causing trouble during the night. They can't see to fly in the dark. If a baby falls out of the box, to the floor, a mean cock will go after it. Sometimes they will even kill it.
Do you have a 2 inch board running across the bottom of the nest boxes? That helps to keep them in. His parents should have protected him from a bully if they were there. So this could be happening after they are starting to leave him alone more. And the other bird could be going into the boxes to hurt the youngsters. At the time this happened, had you checked out all the adults very closely, you may have been able to detect blood on one of their beaks or faces. You need to find out who is doing this. As Renee has mentioned, it could also be a bully, trying to take over the nest box. Maybe you could use more boxs. They like to have choices. Do you have perches for them? That's important. The male normally wants to perch outside of the box somewhere for the night. When one bird is on the eggs or babies, the other is out running around and perching. If you don't have perches, they will try to take over another box to go to when they are out of the nest. How many perches do you have? You should have more than the number of birds that you have. Do you have any adults who seem aggressive? I spend a lot of time with my birds, and therefore pretty much get to know what each one is like, but sometimes even they can surprise me. My loft is built right off my house, and I can watch them through a large window. Sometimes I'm surprised to see one of them do something that seems out of character. Some of our members have set up cams in their lofts, that connect to their tv's or computers, and they can watch the interactions that go on between the birds. It's really interesting to watch. How long have you had them? A lot of people put boards, like low shelves along the walls, where the babies can go under and get away from the adults. Little places to hide.