Does with kits in the nest, rarely have much to do with them. She will go to feed them a few times a day, and thats about it. After years of litters, ive never seen a mother feeding the kits, so dont worry if it seems like she has rejected them. Im sure she hasnt.
What you described as 'stepping' on them, was just the mother guarding her kits. She must have felt you were a danger to her babies, so was standing over them to protect them.
As the mother is obviously upset about you in the nest, take her out of sight of the babies when you check them. Remeber to rub your hands in the mothers soiled bedding before you do so. You only need to be quick, just part the bedding slightly to check if any have died, and that they are all wiggling and warm. Just look at their bellys, if they are round, and the skin on it is faily tight, then they have been fed by the mother. But, if the skin around their stomachs are very wrinkly, then this means she hasnt been.
Youll need to make sure that all the kits are surrounded by the mothers fur, and have extra bedding.
Mind usually start to wander out of the nest at about 2 weeks old-ish.
feel free to PM me if you need to know any more, and GOOD LUCK
Emma x