I've just noticed whenever I'm behind one the trunks aren't centered in the opening...usually shifted to the left.

I have the body panels not being flush issue and the condensation issue. I admit both are very minor and very annoying. I called Scion customer service and they gave me a case number. I have to bring the car to my dealer to have it checked out.

It's not a big deal and Toyota seems like they want to help get it fixed which is nice!

I haven't had any of these issues, but what I did notice and I don;t like is the aft part of the windows get slightly damp inside when washing the car. Other than that My taillights were good and panels fit fine inside...seems this would have been sorted since the car has already been out for awhile in Japan.

can you describe which panels werent flush?

I dont know if its my imagination or what but I noticed this before I even read this. The gap of trunk meeting the rear quarter panel on the right side seems to be larger then the one on the left. Same issue? Im going to take a tape measure to it in a little bit.

Reat trunk lid at the top does not mert flush with fender. Trunk lid is lower. In mine is worse on the right side

Took a tape measure to mine, the right side gap between the trunk and the rear quarter panel is 1/16th to 2/16th of an inch larger then the the left side. Does this warrant me doing something about it? Opinions welcome :]

I've got one issue with mine, my windshield appear to be wrongly wash on the driver side when watch under the sun. But actually it's a defect on it like between the layers. I've try to wash it several time, bring it to the dealer and they try to wash it correcty but was still visible under sun. Next week my windshield will be replace.

Please try and be there when they do this. Most likely the dealership will outsource this job to a third party company so you can probably sit outside and watch. I have had a few botched window jobs and on modern cars its very easy to get wrong and also destroy the clips and plastic that is in the way.

condensation and body panel fit
 

I do to my trunk looks a little off and my passenger tail light has condensation in it that is still there after 5 days. I'm sure that Toyota will take care of it under warranty.

My friend got an FR-S. I noticed when we picked the car up at the dealership that the gap between the door and rear fender is relatively large on the top (where the door window glass is). The gap becomes smaller at lower corner. I checked the other (passengers) side and it did look symmetric though.

Not sure if this is related...

Unfortunately I can't be there, I'm a car mecanic too. But it's not a third party compagny their a guy who do windshield at this place.

I noticed the gap between the fender and the trunk on the driver side is about twice as large as the one on the passenger side. :( I haven't seen the condensation yet because the car didn't get wet yet.

Is the body panel issue only supposed to concern the rear fender / trunk region?

I have check all fits around the front and side of my car, and everything seems to be symmetric. Problem is, this is the first car I have paid that much attention to and I don't know what would be considered an 'excessive' gap.