Try heavily starching the fleece fabric (if you have not already cut out the pieces). It stiffens the fleece so it will not stretch while you piece. If the puckering is occurring while piecing, I am assuming the fleece is stretching a bit as you sew, then springing back so that the cotton puckers. If you can't starch the fleece, placing it on the bottom while you piece may help, as will using a walking foot.
If the puckering is occurring while quilting, spray starching both top and bottom should help. Basically what you want to do is place the quilt on a large flat sheet, spray the starch on, let dry, then spray again a couple of times each side. Using a fan will speed the drying of the starch in-between layers. This stabilizes the fabrics so they are less likely to stretch and distort while quilting, and the starch will wash out later.