Recently had to have top replaced on Jeep (see my thread elsewhere). Noticed the other day as I was putting left window in there was hole in the left sail panel, just past the zipper join. It's covered by the Velcro flap of the window, but it's there. Took it to dealer this afternoon after noticing a row of 5 places in the seam tape of the Velcro that had light shining though. They are holes in top skin, but seam tape covers them up. Service Manager noticed they were also on the right sail and that there was a similar place on right side window Velcro flap. He took photos and is writing it up for a warranty claim.
I walked the lot and checked the only '12 JKU soft top they had and found similar holes, but in different places (same area as mine, different arrangement) and there were none on the passenger side. A few of the '12 JKs had them too. Two had it on both windows, two only on one window. But none had the hole all the way through like the one hole in mine.
Get the feeling we will be seeing a new recall soon.
This pic is from inside, left rear
This pic shows the hole that I first noticed. This is the left rear sail.