There are several different problems discussed in this thread. You mention one of them that tends to get lost; if the usage counter on your phone does not agree with what you are being charged by your carrier there is a problem in the carrier's recording system. The two sources of data should agree to within a few percent.
Data leakage is a separate issue. There will always be some; some of the built in apps can only get data via cellular, because it is routed by Apple through the carrier's network. The most obvious example of this is visual voicemail. There's also some types of notifications. But this leakage is small. It should be around 1-2k per hour, except for VVM messages, which are audio recordings that are sent directly from the carrier's servers, and thus can only go over their network.
Cellular data usage while you are actively using WiFi should not happen, except for the special case I just mentioned. If it does there is something wrong with your phone or iOS, and early reports are that 6.0.1 fixes this specific issue.
Cellular usage while the phone is asleep and not plugged in to power is normal and the way the phone was designed to work for background apps, as the phone turns off WiFi when asleep. All versions of iOS have worked this way; it's to prevent the battery from going flat while on standby because WiFi when on uses power continuously, whether data are being transferred or not.
Cellular usage while the phone is asleep and plugged in should not happen, except for the "background" usage I mentioned in the 2nd paragraph. But the only way you can know is to use a tracking app that records time-stamped usage on the phone, or by noting the usage before and after each period of standby from Settings/General/Usage.
Finally, for most carriers, you cannot tell from their web site or bill when data transfers actually happened. The time stamp on reported data transfers is the time cumulative usage was posted to their billing system, and can represent data that accrued over a long period of time, up to 24 hours. So, except for the total, usage reported by your carrier is useless for diagnosis.
All of these factors tend to get lumped together in this discussion; it would be helpful when posting if you describe which scenario is causing your issue.