Make sure you're holding the rotary cutter straight up and down. When I first would cut, I would hold the thing so it was on a 45 deg angle from the table... seemed like a good idea at the time. Then someone said to hold it so it's perpendicular to the table, right up against the ruler, and otherwise not at an angle. That helped with the pieces.
Oh, and make sure the rotary blade isn't so tightened that it can't move. Another newbie problem for me, I would tighten the washer as much as it would go... problem is that blade wouldn't move freely. So it needs to be slightly loose to move easily but not wobble.