Momma Cat Behavior Problem

The cat had 5 kittens almost 3 days ago. The momma had easy birth and stayed happily with her kittens for two days, then suddenly with no warning, last night she took one of the kittens and removed it to a more hidden place where it alerted me by pitiful cries. I put the kitten back with the others and the momma went for it again growling and agressive. I took the kittens away for a while, later putting them back and putting momma in where she did allow all to nurse. Early this morning I was awakened again by the pitiful cries of a separated baby. Today she separated two of the babies staying with them in the hidden space, 2 left in the box and one abandoned and crying on the floor. I put the kittens together again and she nursed all, then tried it again. Put one away and when I rescued that one back to the others immediatedly grabbed the second one and was carrying it away. Currently I have 'custody' and am not allowing unsupervised visit by mother. I do not understand what is happening.
Can this be resolved? Please help.

If it's the same kitten she is removing or leaving, that particular one may have a problem you can't see and I would take it to the vet for a look.
If she is just slowly moving one at a time to get them to a more hidden place, I would put her in a smaller room and block off any hidden places. Usually they move them if they feel threatened in any way, even if it's not obvious to you. I would also, if she doesn't have one now, give her a laundry basket or something she may feel a little more secure in.