On a long seam like a border, especially if it was cut on the crosswise grain (from selvage to selvage), it might help to use the walking foot. Be careful not to pull or push the fabric through the machine, too. If you are sure that both pieces were cut the same length and you still come out with one piece longer, then one layer didn't feed through the machine correctly. Since the seam is straight, you will end up with one side puffy. So you have to decide whether to fix it or hope it will "quilt out".
I am just now stitching 14" blocks together with my 1/4" patchwork foot and had the same problem on one seam, even with pinning. I'm ripping and remeasuring to double check the accuracy of my 14" and then put on my walking foot before I restitch.
ETA: I just checked my measurements, one block was off by 1/4" at one end. I had to square it up again.