A lot of the discrepency with games is vgchartz only tracks boxed good sales. Publishers official figures they release will include digital sales. Other than that, I dont know what to tell you. The numbers on this site certainly arent perfect, but they arent meant to be either.
They do go back and make a lot of adjustments on hardware, but software doesnt get adjusted as much. Mostly because that would be a huge amount of effort to constantly readjust software totals