Well, I'll be as clear as possible. Most of the time I manual focus whenever possible and use the autofocus assist light to confirm my focus if I am having any diffiiculty - as with eyes getting tired from a long day. This system is about 99.8% effective in bringing home proper focus. On those times when I do autofocus, on my previous 1Ds2 and my current 1Ds3, I have found the cameras to be about equal in getting the job done: a little over 90% with dead-on on static subjects and about 70-80% acccurate on moving follow-focus subjects. My new 5D3 autofocus is about 99% accurate on static subjects. However, I have not yet enough experience to give you a figure for the moving follow-focus, but so far, it looks better than my previous cameras and very promising. Also, on both the 1Ds3 and 5D3, manual live-view focus is 100% accurate when you can take the time to use it.
As for your recent problem witht the group picture, I have no idea what could have caused the specific problem you describe, but here are some possible reasons for the misfocus: light level too low for the autofocus system to work properly without an assist, user error in mis-aiming the focus sensor markings over the subjects, extremely and unusually low subject contrast, lens microadjustment not done or inaccurate, lens or camera focusing systems grossly out of adjustment (needing Canon service repair), accidentally nudging the manual/auto focus switch to "manual" while mistakenly thinking the lens is autofocusing, or even a totally out of alignment glass element from some abuse to the lens. Take your pick.
In my experience, the autofocus capabilities of the higher end Canons, with a few exceptions, are as good as, or better than, the only other autofocus system I'm familiar with - Nikon's. And now - with the 5D3 and 1Dx - Canon's autofcus is at the top of the heap. Do, however, consider the joys of manual focus; it's certainly a technique you could easily use to perfect a group shot of people with very little trouble.
I'm afraid that, in the end, you'll have to figure this one out for yourself.