Everyone's answer is on target. Another thing I learned is...how hard to you press the rotary cutter down? With a dull blade you tend to press harder or even if you are not standing above, but sitting...as you press that blade along the ruler, it is pressing the fabric being cut DOWN...ever so slightly, not even noticable...to the cutter, but that tad bit of pressure on all four sides can cause the measurement to come out nearly 1/4 inch off...little off each side. (Not sure if I said that so it makes sense!) But this is why they say don't cut more than 2 layers, use a sharp blade and stand above the cutting.

The only time I use the lines on the mat is to line up the fold of the fabric (I cut from yardage) to a line, then cut the bottom edge with the ruler, making the first straight edge cut. Then start at the bottom (where you just cut straight) and use that bottom edge and the fold side to line the lines of the ruler up with then start cutting. Annoying that such a tiny little thing can cause a major problem! But just get your system going and you'll be able to cut them just right!