You must be talking about the little foam seal at the front end of the deflector, near the review mirror.
I had trouble with that too with my former 2003 X. One side came out fine, the other side ended up with a tiny gap between the foam and where it's suppose to "seal" against/near the mirror trim. The little gap did not affect the functionality of the deflectors. It was noticeable to ME, but not to anyone else.
Just try to get it to fit the best you can. IF I remember right, it was a question of where the foam part ends up in proximity to the mirror - like it's suppose to bend over the mirrors trim, or a contour in that general area (something like that).
I'd take a closer look at mine, but I traded the thing in for a Fronty Long Bed a few weeks ago!
(For the record: 2nd gen's don't have that issue, as the little foam cushion thingy is not there.)