Mine did the same thing. I'm having it fixed right now while it's all being painted. The stock hinges don't allow for much adjustment at all. The hinge is actually glued to the body if I'm not mistaken. In my case it was actually partially pulled away from the body, causing the door to slightly go out of alignment and creating the problem you are describing. I had to buy new hinges so that they could be adjusted correctly.
Maybe there's something you could do to prevent from having to buy new hinges, but I don't know what that might be. The body-side hinges are about $150 bucks from the dealership. GM Parts Direct has them for about $50-$60 cheaper, but when I ordered them last month, they were on national back order, so my order was canceled. You can also check Ebay for aftermarket pieces that are cheaper. Good luck and hope you are able to fix it without breaking the bank!