My cat had kittens three days ago and is not leaving them to use her tray what should I do to ensure that she is OK

You don't have to do anything, she knows what she needs, wants when she is nursing. It is not unusual.

Our cat (well.. stray cat... ) did the same thing... she would poop in the litter box with the kittens for the first few days until she felt safe enough to leave them on their own then she resumed doing her business in the garden.