A: This is a side effect of the way that iPods and iTunes function. If a song is skipped very quickly (about two seconds or less), it does not qualify as a skip. Similarly, if a song is skipped after more than about twenty seconds, is also does not register as a skip. These behaviors allow users to skip many tracks quickly when searching for a specific song, and also guard against accidentally pressing the skip button in the middle of a song. Also, unless a song is played all the way to the end, it will not register as a play.
To work around these limitations is fairly easy. Let's say it takes you longer than twenty seconds to decide you don't want to hear a song. Simply hit the back button to go back to the beginning, then skip it again after waiting a few seconds. This will correctly register it as skipped. After a short time, this process becomes second nature.