I just did a test and mine appears off a bit as well. However, I did a test where I focused on the extreme top-left corner of a square and fired 3 times. Each time it locked focus properly on the corner of the square and NOT on the wall behind it. When I looked at the playback, the highlighted area was on the wall, not on the square. So I think this may be a playback issue, NOT a focus issue.
It's a misalignment issue. But...misalignment of what? Ideally, the transmissive LCD, the AF sensor, and the image sensor should all be aligned. If the transmissive LCD and AF sensor are in sync but the image sensor isn't, focus point placement for the shot will be correct but the AF point playback display will be off. If the AF sensor and image sensor are in sync but the transmissive LCD isn't, both focus point placement for the shot and the playback display will be off.
I expect careful testing could determine which was off. It's worth noting that the actual area of the AF point on the AF sensor is larger than the little box in the viewfinder. Spot AF uses a smaller area of the AF point, but even that is slightly larger than the box in the VF (the main box, not the smaller inset box that indicates Spot AF).