Try playing the song again and if it does it in the same spot on both your ipod and itunes then you have a corrupted file. You need to re-download the song. Don't worry, this is free if you bought it on iTunes. First, verify that you did buy the song on iTunes and not anywhere else. Go to the iTunes store. On the right hand side of the window there is a column named quick links. Look for "Purchased" about 2/3 of the way down. Click on it. The next window that shows up should show you all the tunes you have bought. Find your tune and you'll see that is says "downloaded." Now you know you have the tune.
Now go back to your music library on the left hand column of the window. Click on Music. Find that tune that is giving you the problem. Delete the song.
Now go back to the iTunes store like before and go back to your "purchased" list. The page needs to be reloaded Press the back button and then click "purchased" again on iTunes so the list reloads. Find your tune again. Now instead of it saying "Downloaded," it has a picture of a cloud with an arrow pointing down. Click on it and the tune will download again with, I hope, no problems. I hope this helps.