Are they in the pouch when your approaching them?
Sounds like they are scared, possibly pouch protective. Try Open Environment pouches for them.
Start a daily routine, same time every day do treats, talk to them when approaching the cage, bonding bag same time same time every day. Joeys are like human babies, they learn the routine quickly and will soon know all this is normal and come to expect it.
Also could be getting hormonal/sexually maturing, neutering might help. Which is probably why dad is getting more aggressive towards them. If neutered soon they could probably go back in with mom n dad with close monitoring of course. If mom n dad continue to breed the boys will fill in as babysitters to give the parents a break
IF the neutering resolves dads aggression.
I wish I could help more, I've had 3 joeys here n never had that issue the only time any of the joeys crabbed was when I handed Cozig to a friend of mine.
She was fine for like 2.04 seconds, looked at me then looked at my friend looked at me again and came unglued crabbing her little face off when she realized she wasn't in my hand
she was like 5 months old never heard her crab before that so it kinda shocked me lol. I took her back n settled her then tried again....... same response only a lot faster lol she's a Momma's girl through and through