I think Live View doubles the shutter count, since the shutter must open to view, then close and open again for the exposure.
Other than that, I'd imagine there are a few other cases such as HDR and long-exposure noise reduction that also fire the shutter more than once per shot, but I tried the count with Live View, and it seems that's the likeliest culprit.
edit to add: by the way, I did actually try this on my D7100, and it does appear that the shutter count goes up by two for each LV picture. I rarely use LV so had not really thought about it. But if you think of how LV works, it makes sense.