Are you quilting on a frame or a stationary machine?
If on a frame are you floating your top or loading it on the bar intended for the top? Sometimes floating can contribute to this problem. Also are you making sure when you baste the top of the top to your loaded backing and batting are you ensuring it is square when you do that first basting line?
The quilting itself will cause a bit of drawing in on the top but it sounds like your initial baste across the top is not square. For the most part, if you are allowing yourself enough excess backing and batting, the issue you are experiencing isn't going to cause problems.