In my experience it's typically a lack of skill. I've had to mentor people on being better communicators, and some of the typical problems I've seen along the lines of your points:
* They don't know how to politely communicate that they don't understand the question or disagree with the premise. The mental transformation from "that makes no sense, I don't understand what you're asking about" -> "I may be missing context here, but..." isn't something that comes naturally to everyone.
* They don't know precisely how focused they should stay. Sometimes the discussion really is too narrowly scoped and needs to be broadened, and it can be hard to calibrate.
* They don't know how to prompt other people, who may have a very different sense of which angles are relevant or how wide the scope of a conversation should be, to focus back down on what they need to talk about.
* They don't know how to politely communicate that they don't understand the question or disagree with the premise. The mental transformation from "that makes no sense, I don't understand what you're asking about" -> "I may be missing context here, but..." isn't something that comes naturally to everyone.
* They don't know precisely how focused they should stay. Sometimes the discussion really is too narrowly scoped and needs to be broadened, and it can be hard to calibrate.
* They don't know how to prompt other people, who may have a very different sense of which angles are relevant or how wide the scope of a conversation should be, to focus back down on what they need to talk about.