There's a variety of reasons on why babies are ate. Not enough food, you're messing with the babies too quickly and upsetting the mother, not enough space, etc. You may way to pull the pregnant female out, although, I will warn you, attempting to put her back in will cause a ansty cat fight, so clean the enclosure before you put her back in, and make sure she's in the enclosure first before you put the others back in.