Everytime I close my passenger side door the window hits the molding above the window, I have to push in on the top of the glass to get it to go under that molding. Sometimes with the door open, when I roll the window up the rear of the glass goes up about an inch past where it should stop. Whenever I wash my car, water comes in from the rear of the glass too. What can I do to fix this??

 

This is a universal Hyundai problem, though usually not as extreme as yours! the fault seems to be that the seals are not deep enough to act as a guide, or even to seal properly if the window does run home true.
There has been an amazingly long thread about this on the Hyundai Performance.com Forum with the outcome that all that can be done is to keep pestering your Main Dealer.
Side window deflectors MAY help!.

 

GO TO THE DEALER and get your pass. window re-aligned, it's a PITA to try to do it yourself. There are like 4 adjustments you can make