If I am starting out with a 9 1/2" unfinished block (3 1/2" squares) and you cut it twice, you will lose 1/2" both ways and end up with a 9 inch block, 8 1/2" finished.
If you cut each square at 3 5/8 inches (1/8" larger), your overall block will be 1/8" too big. You could then square it up and shaving that little off each side (1/16") would not be noticeable. And you would end up with a 9" finished block.
So you could add 1/8" to any sized 9 patch square, slightly trim and get the finished size that you want.