Since the MRTG graph will show an average over the polling window, but a direct query of the device will give you a point-in-time view, you are unlikely to get the exact same values on the graph and when you look at the device. For example, you might eat an average of one chocolate bar per week; does this mean something is wrong if your wife watches you and sees you've eaten a whole bar in one day?
To understand the inner workings of the MRTG native-mode .log file, you can see some documentation on the MRTG web site
http://oss.oetiker.ch/mrtg/doc/mrtg-logfile.en.html