It means you are trying to ease in too much fullness in the bottom layer.
Do you have a link to your post with the photos? If I am remembering the right photo, it looked to me as if your cutting and seam allowances might not be sufficiently accurate. If they aren't, the rows can be insufficiently accurate to be sewn together without ripples.
Starching fabric before cutting can help a lot with accuracy, but I think you got the squares in a swap? Even then, using spray starch to "block" each square to an exact measurement before sewing them together can help.
Also check your sewing machine. Cut two long strips exactly the same length and sew them together. If the ends don't match, the machine may need adjustment and/or you may need to modify how you sew seams to compensate for this.
What size needle are you using? And what brand of thread? Sometimes these can make a difference in rippling of seams too.