A soft top is a lot harder to keep water out of than a hard top. I can speak from experience. My hard top leaked on the day of delivery and the dealer couldn't solve the problem after 50 pages of modifications. Then the Chrysler rep looked at it and put me into the vehicle buy back program. My new jeep leaked in the exact same spot. They adjusted it twice and it hasn't leaked since then and it has been almost three years. They made me a satisfied customer. I can't talk about the details of the buyback as I signed a gag agreement that I wouldn't. All I will say about my situation that led up to the buyback is that I felt that the dealer listened to my issue, tried really had to find the problem and repair it, and when they couldn't, didn't need to be threatened. As a customer, I gave them many more opportunities to fix it than the lemon law required in Massachusetts. Maybe that is why I didn't have to threaten them with a lawyer. I really just wanted it fixed.
All that having been said, I will add that I have both tops. When the soft top has been on my jeep, I have had leaking problems. They have always been solved by me by just adjusting it until it sealed. In your situation, there may be more than just an adjustment issue such as a leak in the top itself. I hope they find it for you and make you a satisfied customer.
Now that my jeep is no longer under warranty, I have different expectations about leaks. You haven't reached this point yet (I don't know how long you have owned it) but, it is after all a jeep. There are a lot of seal surfaces on any jeep, all of which have to work, to be able to keep water out and prevent the rug from getting wet. As a maintenance item, to keep your jeep from leaking, try using a product like Turtle Wax Ice interior cleaner to keep the seals clean and lubricated. When you do this, the seals slide easily against each other and the lube (typically silicon) will help to keep water out. I do not recommend any oil based products like Vaseline as that may eventually deteriorate the seal. The Turtle Wax Ice interior cleaner has kept my seals looking new and sealing well. The idea of using a lube on my seals was suggested to me by another jeeper with a JK who I bumped into while camping in Maine. I told him that after the dealer solved my leak problem I would try this. It has worked for me so I'm passing it along. Best of luck to those who are having problems with leaks. If this solution helps be sure to post back about how you solved your leak.