This is actually a feature of HN. There is a "cool-down" timer between when you make a post and when people can respond to it. It increases exponentially with the level of nesting. The idea is to discourage flame wars by forcing people to think a bit before replying.

I actually think this is a pretty effective strategy. However, it does impede productive discussions and conversations, sometimes. Oh well, c'est la vie.

But instead of waiting, people just reply in the wrong place which both defeats the purpose and makes threads harder to read. I can't think of any better solution, though.

To expand on tikhonj's comment, you can circumvent this "feature" by clicking on the "link" link next to someone's comment - that will allow you to reply to them regardless of the "cool-down" timer.