I have the same problem... sadly I can't give you comforting advice. My cat, Izzie gave birth 4 days ago to 7 kittens (her first litter). There was a runt, but I took special care to make sure he was always getting food, and he was happy and thriving.
I did notice that she would sit on or lay on them at times, and I barely slept the first 2 nights in fear that they were going to suffocate, so every time I heard a scared mew, I woke up to make sure no one was being squished, and if they were (a lot of times this was th case), I moved them out from under her and placed them to safety. It was like she didn't even notice or respond to the crying.
I decided to spend last night with my boyfriend as I hadn't seen him in a week, and I figured Izzie had gotten the hang of things. When I came home this evening after a long day of job-hunting and the like, I found one of the kittens squished and dead. :-( I was shocked and upset at realizing that she had done this. Upon further inspection and removal, I realized it was the runt (who I was affectionately calling Scraggly due to his hair). I'm still crying about it, because I was especially attached to him, and was planning on keeping him out of the rest of the litter.
All I can say is to give her a bigger space (maybe that will prevent her sitting on them), and when you are around, see if you can somehow make her better aware of the babies if they are under her. I hope they remain OK... I feel extremely guilty for that poor baby.
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