I almost always use software, but one problem that has given me is that I suffer a little in music theory. It's not that I don't know how to read music notation or symbols, it's more that I do everything by ear. Right when I place a note (I move it up and down until it sounds right), and so I'm not great at seeing or figuring out where the notes really fit into a scale or where that scale fits on the staff. This in turn makes my music suffer some (don't get me wrong, I do fine by ear). It limits my compositions in certain ways.
Of course, I can be lazy when it comes to music theory :P