Pictures are always helpful.
If, however, your squares are already cut, and depending upon how stretched out of shape they are, it's not a lot of fun trying to get all the diagonals to match when joining blocks together, and keeping it all square.
So, are you sure you've cut them all the same size?
Are you pinning the intersections before joining the blocks?
And, sure, you could always put a border around each block, square up all the blocks to the same size, and then join them together.
You lose the design as presented in the quilt, but maybe using a variety of fabrics to border the squares, you get a different looking one.
Or you could join, say, 12 blocks together, press and starch those to lie flat, border that piece, and use that as a building block in the quilt.
Again, hard to say without seeing a picture showing the condition of the blocks.