I am guessing that you need to check your seam allowance. Here's a good reference:
http://www.quiltingboard.com/tutoria...ce-t89997.html
With a rail fence, if you sew long strips then cut, rather than using the measurement in the pattern to cut the squares, measure the width of your sewn strip set and use that to cut the squares. If your seams are off this will compensate.