The Discussions feature is widely used but the navigation tools are very limited and not well placed. One consequence is that students frequently "Reply" to the last entry in a topic when what they really intend is to start a new thread, but that requires them to scroll back to the top & click "Reply" in the topic pane (see image below). (Others have suggested differentiating the two kinds of reply, also a good idea.) There have also been excellent suggestions for visually signalling the nesting of replies which is curiously absent (yet ironically, implemented in this very forum).
Here's my simple suggestion: The navigation tools should always be available (i.e. visible), rather than embedded in the the top part of the topic view. Specifically, I recommend moving the navigation tools from the top pane of the Discussion view to a location that is always visible, so users don't have to scroll all the way to the top to initiate a new thread in the topic by clicking the correct "Reply" button, expand/collapse, view unread, etc. This could be a "sticky" navigation bar somewhere in the window, a floating palette, or something similar.
Topic pane example (appears at the top of the Discussion)