Based on my experience, the iPhone records all data sent and received, including data exchanges which you are NOT billed for. For example, if I reset my useage states at night, turn off wifi, have all email and such sent to manual data access only and nothing else running, there will still be cellular data exchanged during the overnight period - never more then a few hundred Kb, but still recored under useage stats nonetheless. To the best of my reckoning, that data never shows up on my billing statement. But, it does mean the iPhone will always be showing more data sent/received then I am actually billed for.
P.S. exactly what the non-billed data is, I don't know nor really care. Some sort of house-keeping or network timing data???