When I pin the sewn together squares to make rows I first put a pin through the seam that's already there and turn the piece over and see if it comes out the seam on the other side.
If it does then you are good to go, if it doesn't reposition the fabric and try again.
I may not be explaining that well. :-)
Second try:
Lay one row of 3 sewn together squares right sides together with another row of three sewn squares. Poke a straight pin thru the first seam where the first and second block were sewn together. The pin should come out the back on the seam line of the bottom blocks. Leave that pin in if it's ok and do the same to the next seam then sew the two together. Maybe that makes more sense. Don't sew if they don't line up. Adjust.
I hope this helps.