One of the biggest problems that I see on a day-to-day basis on the lesson tee from the more experienced golfer is faulty alignment. I see students trying to fix their swings when their biggest problem is not knowing how to aim. Granted, you cannot always go straight at the flag stick because of a cross wind but with proper alignment from the start, you can take wind direction into consideration.
I think many players know subconsciously that they are set up right or left of their target and either get over the top and pull the ball back toward their target or block out their follow through and try to push the ball out toward their intended line.
To learn how to align yourself to your intended target think of railroad tracks. The track that the ball is setting on should be on line with your target. The track that your feet are on should be on a line parallel to the outside track all the way to your target.
Jack Nicklaus had the easiest way to line up. He drew an imaginary line from his ball to his intended target and that line crossed over a piece of grass or imperfection on the ground about two or three feet in front of him and he aligned the leading edge of the clubface to that spot and then he took his stance. This is a method that you can trust and not worry about your alignment during your swing.