I have a Canon EF 70-200 f/4 L and a 5DmkII. I've used this setup regularly for awhile now, and I've come across something I can't quite explain. I recently shot this bridge in Oregon. I used a sturdy tripod (Manfrotto ballhead/tripod combo), so stability isn't an issue. Still, several of these images came out much less sharp than I've been used to seeing from this lens. It looks like motion blur to me, but like I said, I was using a sturdy tripod. I shot at f/8, and even one of the images at f/11 had this same issue. Shutter speed was 1/20 and ISO was 125, and autofocus was directly on the front of the bridge itself. I can't imagine this lens is suddenly misfocusing so badly.
You say that several of your images came out blurry, which implies that others did not. How do the settings compare between these two sets?
I would suspect mild shake due to the wind or the mirror flipping up. As others have suggested mirror lockup could address this. But it might just be that your AF had a rough day. Did you try manual focus as well?