The red square means the focus point was active at the time of capture, black square means it wasn't. Eg, if you are using AF-On to enable focus but let it go the AF isn't active when the image was captured (and all you'd need to to is sway a little on your feet forward or backwards to through the focal plane off the subject).
Since there's only one point showing in your image above, I'd hazard a guess that these images were captured in live view with a single point selected and you have AF removed from the shutter.
I've been sweating these results and have learned a bit in the last few hours. I think I've solved it now - might be trivial for many, I guess.
Yes, I was using back-button focus. I let go of the button after getting focus. No need to keep focusing once it's focused, is there? But somehow the focus must have shifted, on every single shot taken that way, and those shots are all soft. For the last few, I must have kept my thumb on the AF-ON button while clicking and got good focus in those.
Phew, so it's not the 7D2 or the lens. Nor was it hand-holding a long focal length, nor the vibration of the car I was in.
This was the first time using BBF for me, and a good lesson on how to do it right.