Take it to the dealer its cover I got mine "fixed" 3 times almost every winter. Just started doing it again but no more warranty for me lol.

 

I had this EXACT problem with my drivers side and I can tell you from personal experience, there is only one fix for this... Go to the dealer, dump
The water out on the ground in front of the service manager as I did and they will order the new, update freedom panels... My '12 leaked from day one, went in and did my magic trick with the water appearing out of the top and BOOM!!! New freedom panels..,

Nothing but a manufacturing malfunction causes this... The new ones have an updated seal that comes with the tops...

Over tightening the top does NOT cause it to fill up with water.. The top itself is bad... PM me if you have any questions...

 

I had issues with leakage as well that got blamed on the hardtop but they were into the cab onto the floor. Turned out to have nothing to do with the hardtop or tightness of the bolts. So i think that is a bit an excuse that chrysler is making to make people feel better. But to the point here it seems like we have a few winter drivers on this post so my question to you is have any of you found that the hard top creaks and squeaks as you drive and go over bumps? I'm from Alberta and yesterday it was about -25c it was a little noisy till I got the cab warmed up.