Since the sights are above the gun, there is always an incline if the gun is zeroed at any range. When you launch a bullet upward at any angle less than 90°, the bullet will follow a parabolic arc. When you adjust the sights to incline the boreline just enough for the very top of the parabola to touch the Line Of Sight, you may be said to be sighted in for that distance. For every other distance, you will shoot below your point of aim. Now, adjust the sights to incline the bore line just a little steeper, and the top of the parabola will extend above the LOS. You are now sighted in at the point where the parabola crosses the LOS the first time on the way up, which will be closer than the peak of the arc, and again where the parabola crosses the LOS second time on the way down, which will be further away than the peak of the arc. Between those two points, the bullet strike will be above the LOS. Closer than the first zero, and further away than the second zero, the bullet strike will be below the LOS. If you adjust the sights to incline the boreline a little steeper still, then the first zero will be closer, the second zero will be further away, and the peak of the parabolic arc will be higher above the LOS.
Given the same ammo and the same height above the boreline for the sights, it makes no sense for a gun sighted in at 100 yards to be dead on at 50 yards, but for a gun sighted in at 50 yards to be 1.3" low at 100 yards. However, much of the discrepancy could be measurement error.