I am doing a quilt now that has flannel in it (it had the exact color and pattern I needed.)- a quilt for me! I starched the fabric after washing and hung it to dry. I am adding some starch when I press it. Then I am cutting. That should keep it from misbehaving.
Remember to press (up and down) and not iron (sliding along).
Don't know how to fix the ones you have already done but do not give up on flannel - starch is your friend! Use it before cutting your blocks.