Squaring the blocks up certainly helps. Starching fabric before cutting, starching as you sew and iron, and starching finished blocks all help to keep block edges from stretching and distorting from handling (and ironing).
I am wondering how you handled the rows that didn't quite line up. The first thing you need to do is pin the rows together using a pin at every block intersection. Often there will be some blocks that are bigger. These need to be "eased in" to match the smaller block. If, instead of easing the bigger block, you stretched the smaller block, this can make the finished row wavy. "Easing" is a sewing term you can Google for a better explanation than I can provide here.
Whenever handling quilting pieces, including blocks, you want to be careful not to stretch edges. Edges of pieces, edges of quilt blocks, the edge of an unfinished quilt top, border edges, etc. are all more vulnerable to unwanted stretching and distortion than the centers of fabric.
If you could post a photo, that would help. If the quilt top does not lie completely flat, this isn't necessary a disaster. Often some of this will go away when batting and backing are added. Also, depending on how it is quilted, quilting can help "quilt out" small errors. Hard to tell how much of a problem you have without a photo, though.