I have found several errors in quilts I have made by taking a picture of them after I sewed them together and before quilting. Yes, I ripped every seam that was sewn wrong. I don't know why I can see the errors in a picture when I can't see them live.
I love the idea of the tree. You could enlarge the idea to include some branches with no leaves, kind of like this long winter we are having right now. I would do some thread painting on the tree before you applique it, that way it will look like it is quilted but be different. I am going to love to see what you come up with to fix it. The quilt is gorgeous but will look much better when the wrong squares are covered.