I disagree with 1 but agree with 2 and 3. I noticed that as well and those were some of the only things I didn’t like. I also thought that Paul should have said the “fear is the mind-killer” speech like he does in the trailer, but they only have Jessica say it and they make it seem like it’s something that you do out of weakness, and not a representation of training and strength.
I’m not sure where you would put it, maybe when they’re flying in the sandstorm or maybe during the march into the desert with the Fremen at the end.