Joel, this is my best guess as to what happened. I haven't had a chance to test my hypothesis.
I think the problem is "Face Priority."
Nikon states in the D4 manual (p. 53) that "(if multiple faces, up to a maximum of 35, are detected, the camera will focus on the closest subject; to choose a different subject, use the multi selector)"
The D4 manual also says (p. 64) "Note that the number of subjects that can be detected in face-priority AF drops in movie live view."
I can't find in the manual precisely how many faces that the D4 can detect in movie live view.
I think it's possible the D4 Face Priority was overwhelmed by the number of people in the pews and as stated on page 53, defaulted to the closest subject who was in the pews. I'm not sure about the indicator yet. Remember that in movie live view, it's easier to overwhelm Face Priority than when shooting still shots.
All that being said. Can you describe precisely what you saw in the monitor as per how the camera indicated it was focusing on the bride and groom? That will help further thought.