I haven't tried it, but this method looks interesting:
Welcome to the Quilting Board!
I have stretched fabrics more than you can imagine to get them to fit. If you really study your seams, I bet some of them have let one of the fabrics slide a bit. At least that is what I find when they don't want to fit perfectly. For the small amount you are off in the above squares, I doubt it would be noticed in the quilt unless someone goes row by row checking points. When you quilt it, it will show even less. I love your scrappiness and I had to really look to see what your tiny little mistakes.