Chicks don't like brooders that open from the top, and human hands reaching at them from above - it triggers their fear of death from aerial predators. Looks like you figured out a better way of picking them up - very good! If you brood chicks again in the future, consider a brooder that opens from the front instead of from the top, and place it high up on a table so you can look straight across at them, not down at them. They'll be less afraid that way.
I couldn't agree more with what Chicalina said! Get them used to sounds, sights, movements, everything. Put them in a dog crate and take them outside for a walk. Put them in the back yard for a bit, near the street so they hear cars honking and trucks rolling by. Mow the lawn. They need to get desensitized to the sights and sounds of life. And handle them - a lot! Especially if you intend for them to be pet chickens and not just livestock. Lots of people have chickens that can't be caught, and that's normal because chickens are skittish by nature. However, I think it's important that you are able to catch and handle your chickens purely for safety reasons. The day will come when one of them will need help - to be rescued out of somewhere they got stuck, to be given medicine, to be quarantined, etc. You need to be able to handle them to take care of them, and it's SO much easier if they are calm and socialized and not fighting you. Easier for you, easier for them. So start working on them now while they are still young, and be persistent.
My chicks from last year were brooded inside the house, next to my young kids' bedroom. Those chicks have seen and heard some sh**

Screaming and tantrums, loud toys, rough little hands grabbing them (being careful, but still, only managing preschool-level careful). The vacuum cleaner! When they went outside, I hadn't finished building their run yet. So I built it around them with all kinds of power tools, including a circular saw. The kids had hardened them to sound so much that they were completely unfazed by the construction! In fact, I had to keep them away from the drill because they wanted to peck at the spinning bit

I could mow around them and they wouldn't care, they'd just wait for the grass clippings to eat. They are 1+ year old now and nothing bothers them. I can pick them up and do whatever I want. They let my kids pick them up and snuggle them. One just finished raising chicks - I could reach under her and take eggs out, later take the chicks, and she let me do whatever (broody hens often turn very protective and mean and attack anybody who dares come close, let alone touch). So trust is also very important and pays off, as a product of extensive socialization. It makes everything smoother and easier. So get the vacuum out and go snuggle those chicks!