Advice please

We had an unplanned breeding and the baby is now out of the nest eating and fully feathered the past day I have noticed the dad being kind of mean to the baby trying to pull her off the side of the cage or sitting directly on her on the side of the cage trapping her in the corner and some of her feathers are missing on her head is it time to get her her own cage or is this something that will resolve itself also she was born missing a few toes and still doesn't have flight feathers I'm not sure if that would cause the parents to be mean to her now that it is time to start flying

Yes, you must remove the baby immediately, before the father/parents kill him...this happens frequently, and is an example of why you always must be ready to take-over raising/feeding baby birds that you are allowing the parents to raise...

Is this baby fully-weaned? You mentioned he doesn't have all of his feathers yet? How old is he? Has he been living outside of the nest-box fully, or is he still staying inside of it? You have to make sure that you house him properly and also feed him properly, depending on his age...He may still need to live in a Brooder and/or be hand-fed formula, depending on his age, whether he's fully-weaned, fledged, feathered, etc.
But either way you must get him away from the father..

You may find it much easier to simply remove the father from the cage if this baby is still being fed by the mother, and still living in the nest box for heat, etc. That way you don't have to take-over...As long as the mother isn't also attacking the baby...that's what I would do in this situation if the baby is still dependent...