It's actually quite hard to notice unless you hold the camera a little bit away from your eye and try to focus directly on it. In the photo above, I did my best to bring the... thing... into focus with my other camera. I had max out the affected camera's dioptric adjustment knob to get the image above.
The image below best represents what the "thing" looks like when you look through the viewfinder yourself — it's the dark splotch on the upper-most AF point.
The "thing" does not show up on images. And it does not seem to be on the mirror or focusing screen (see image below). When I tilt the camera slightly from side to side or up and down while looking through the viewfinder, there is a parallax effect, the "thing" appears to be between the viewfinder lens and the focusing screen (the AF points move a greater distance than the AF points when tilting the camera).
What could this be?