need help/ passenger door mis aligned?

2006 jeep wrangler unlimited front passenger door was leaking so I ordered a aftermarket part off ebay and replaced it. it was a easy fix however the trim seemed very firm and the door wouldn't close without a firm closing it. the trim started to tear and now was bulging on the sides outside the frame so I went to the dealership and purchased a new one and they put it on today. they then thought the door had loosen and stated they could align the door correctly and maybe the issue was never the door trim. A hour later they stated they couldn't get the door to align and it still wouldn't shut correctly. they asked if I had been in an accident. ive had the car 45k miles and 8 years. purchased it at 16k. then they asked if I've taken the hard top off and its only been off once about 5 years ago. the dealership is stumped about the issue. Has anyone else had the issue? Dealership thinks maybe my frame but that just seems weird. any help or insight would be great