How many chickens do you have in that coop/run, including your broody mom, and how many square feet is in your run and coop? If there is stress due to space issues, that might explain the killing.
I can't tell if a predator got the chick or not, hopefully others will chime in.
Do you have an...
I think the only way to know for sure what's going on is to candle the eggs. There are Articles that can help you know how they look during different stages of development (search Incubation and Hatching section of Articles). If you can get a very high lumen flashlight and a very dark room (or...
The chicks could have been killed by the broody mom or by her flockmates, or by a predator that would leave your larger chickens alone. Do you have pictures of your setup, broody enclosure and nest, and of the dead chicks? We might be able to give better suggestions once we see what you're...