Hi,
It happens to all of us. Did you by any chance cut your borders on the cross grain of the fabric? If you did they have just enough stretch in them to allow them to wrinkle as you sew. Even a walking foot might not solve the problem. The reason that garmet patterns have big arrows to indicate the layout as it regards to grain is that the proper hang of a garment depends on how the fabric is cut. Remember that the only place that stretch is a good thing in a quilt is the binding. It was many years before I knew that you don't cut your borders by just sewing them on and cutting off any excess. You have to take an average of the crosswidth of the quilt in several places and cut your cross borders that length. Then you ease the border and the body of the quilt together letting your feed dogs ease in any differences in the two peices. We have all seen quilts that look like the last border is a ruffle. That is what happens when the borders are not cut on the "straight" of the grain. Depending on who will be using your quilt it may not make any difference. A loved one will probably love it no matter how disappointed you are in it's appearance.
A reputable quilt judge would grade the item down if the borders ripple.
I have resorted to couching decorative yarn in the ditch of my quilts that had what I considered flaws in points matching etc.
Unless your quilt is going to be judged by a professional I wouldn't worry about the wrinkles. Just be glad you finished it and didn't just create another UFO.
Mary