One way to deal with the difference is to fold both pieces and crease at their midpoints, matching up the midpoints when you sew them together.
Another way to solve the problem is to trim away 3/8" from the tip at the end of the two long sides of the triangle -- tips often referred to as the "dog ears." Align your rotary ruler as shown, adjusting it to remove 3/8" along each side. Now the side of your triangle should match the side of the square or rectangle that it's being sewn to.
Try it with paper first if you'd like to experiment.