Continue pinning all the way to the edges of Fabric A and B. 
Turn over what you just pinned and make sure you don't see any puckers. If you do, then take out the pin where the pucker is and reposition the fabric in that spot to remove the pucker and re pin. It might be necessary to take out two or three pins to reposition, but not always. Once you are happy then sew the pieces together...going slowly...I leave the pins in and go very slow. Make sure to do the back stitches at the start and finish.
When you are done take out the pins and open up the pieces to make sure there are no puckers.
If you find a pucker then simply pick out the stitch above the pucker and maybe one on each side of it...see if the fabric can be adjusted to remove the pucker, pin and resew that small area. Back stitch. 
These sixteen 3" (that's without a seam allowance) squares you make from this process should look square! If they are not, then now is the time to fix them. My square on the right was the one with a pucker in it, I fixed the pucker but see the top edge of Piece B doesn't line up with Piece A. The difference is less than the 1/4" seam allowance so will not show on the finished product. I will leave it and adjust as I sew it to the next square by using the white fabric of Piece A as my sewing guide for 1/4". When you are ready to assemble the squares remember the most important points to get right on are where the seams will meet. These will jump out at your eyes and be the first thing you see if they are off.
