If you're talking the upper one that starts at the mirror and works its way around to the rear of the door halfway down, join the club. Both of mine have been shrinking since I bought them. You get a bunch of wind noise at the mirrors too when the gap is exposed.
As a temporary measure, you can gently pull it all out, and then put it back in under tension so it fills the whole area. Mine shrink back in a year or so though.
I will have to check the Syracuse junkyards next time I go to see if the northern cars don't suffer the same amount of shrinkage.