When installing wood roofs, it is very important to ensure that the joints in adjacent rows do not align. Sidelap is the distance from one joint, to the joint in an adjacent row. The minimum sidelap is 1.5 inches. The joints in alternate rows should not align either. When the joints align there is a greater chance of leaks to occur. Most roofers understand this, and I have never seen a roofer install shakes with the joints aligned.
However, sometimes the shakes can split due to hail strikes or other causes. Sometimes, this can result in the joints of the shakes to be aligned. In the photo below you, the middle arrow is pointing to a split shake. Now, the joints in the three rows are aligned. As the water gets in at the top joint, it will have an easy path to the attic below. If you have a leak, this should be something your inspector should look for.