I hint I read the other day but have not tried. Sew to within a 1/4" of the centre on the first set of seams press as an open seam or rotate all seams in same direction before you sew across the last full length of centre. Press centre with thumb to flatten. I have seen ladies with a hammer flattening centre. If still bunch try carefully taking out some thickness with scissors. If not lined up put appliqué on a flat centre.
Hope these ideas help. Undoing the seams you may have stretched them by now so check size etc before resewing. Good luck.