This is not something new. You can go to any jeep forum and there will be people talking about this. I picked up my jeep about a month ago ( 2011 JK Rubi ) , and the very first rain, the same spot as your was wet.
My 06 TJ did the same thing but I ended up pulling the carpet and put one of those bed liners in.
If anything it's the door seals. But if you have the soft top it could also be that.