funny you post this up. i've had wind noise around my driver door since i've owned the truck (feb 08, 2005 EB). the dealer and my body guy both kept it for a day each and couldn't find where the wind was entering.
well, i took matters into my own hands and found the piece you are referring to imbedded down inside the black piece of trim. so, i dug it out, filled the void with black RTV, reinserted the piece or black ABS, and let it dry. i barely have any wind noise now.
check to see if your little piece of ABS simply fell down into the trim.
Berry, how do you come up with this stuff?? Hah.. You are the man when it comes to noticing flaws in the Expedition! I just checked both my driver and passenger doors and both have the piece pushed into the trim. The whole design looks like an after thought.. This is definitely the kind of thing that separates the japs and the germans from ford, poor fit and finish. I will be mentioning it to the dealer at my next oil change as I am definitely not going to spend my own time and money trying to seal those holes.
Don't get me wrong I love my truck, but petty little things like this **** me off.. They just should not happen!