Hi all - I'm having this same problem. My 2012 Focus has been into the dealer twice (in Canada), and they don't seem to be able to figure it out.
I'm able to reproduce it easily:
1) At a car wash, holding a hose on the door for 4-5 minutes. Open door, lots of water comes out.
2) Rain. It won't drain out over night either. It rained here on Sunday, and when I opened the door on Monday morning a fair amount of water came out.
This is really an odd issue, and I can't understand why it can't be fixed? This cannot be normal. I'm worried because it is getting cold here, and the water inside the door will easily freeze soon.
How can it be normal when it's only one door? The other rear door doesn't do it, nor does the driver side door.