This does not sound possible, getting lines when copying through glass sounds pretty weird, try cleaning the glass several times.
If this is not the solution, it could be the imaging units or the Scanner itself which is a big problem.
Kimzi is right! The problem only can be at the glass. To make sure is from there, do a quick test. Do a copy using the document feeder and then do a copy from the glass. You may see that the problem only happens from the document feeder.
You will see a small glass on the left side and because is very dark you will not see the dirty spot. Grab a light and try to see where is the spot.
Use water to clean the small glass.