Leave it. Chalk it up to your longarmming education tuition. I had it happen once, too. Mine was only at the very bottom, not a long pleat, for a family member, I left it and said nothing. No one knows it's there but me.
To prevent it from happening again, I adopted a new way of handling battings, which works beautifully. After loading the backing, I attach the batting across the top with stitches, then smoothe it with my hands onto the backing, a little at a time, rolling both onto the takeup bar as needed, all the way to the bottom, where I use flat head flower pins to attach it to the backing across the bottom. Then roll back up to the top and stitch down the quilt top, proceed to quilt. The batting rolls right along with the backing as one unit and I never have to think about it again. I have never had a pleat or pucker in my batting after I started doing this.