If it is a new jeep, let the dealer work on it. With a door leak, it is either a door surround that is not properly seated or misaligned door or the seal itself has some defect. Whatever the cause may be, the dealer should help you out on the cure.
Participate in life....Keep movin'....Go there....JK'n it.........Do it! Jeep #1: Red Rock 08 JK Rubicon 4dr, 6 sp manual, Stock Mud Tires, MyGIG Upgrade, Hard Top, after sale BestTop SunRider Soft Top, Congo Cage Rack, Mopar slush mats Jeep #2 Black 08 JK Rubicon 2dr, 6 sp manual, both tops, some chrome...uggg (my wife's jeep) Jeep #3 White 92 YJ (my son's jeep) A great quote from a good friend: "All hail click clack and master jk'n." Click and clack are my idols!
I have a 2010 soft top and the passenger side is horrible. Actually today, there is a small lake on the floor. I have made sure that the door molding is seated properly (still can't get over the fact that you can just pull it right off) and that the top is on right. Doesn't matter. The inside of the door will be soaked and the seat and floor are just sopping wet. The driver's side doesn't leak; it just pours in, from the roof, when you open the door. I know that it's a jeep and it is meant to get wet, but I shouldn't have to get a well a@@ whenever it rains.
My 2010 Sahara had the exact same thing day one and I took it right back. The dealer added silicone to the bottom of the A-pillar right where it meets the door frame and it had never happened since. It maybe a known issue with soft-tops