Data is collected from select retail sources and then extrapolated on a national (regional) level.
This is the same thing that NPD, Chart Track-GfK, Famitsu and Media Create do. Because all tracking firms use sampling (extrapolations and algorithms) and cannot track sales on an individual per unit basis, a margin of error exists for all of them. Because of this, none of them are "correct".
Also to keep in mind, Sony, MS and Nintendo report shipment figures every quarter. These figures will always differ from the tracking firms (including VGC) because they track consumer sales and a gap will exist between product on store shelves, in wharehouses and in transit (games are usually shipped in container ships....and that takes a minimum of 2 weeks).
So how accurate is VGC? Let's just say that it gets more accurate every day as the sample data grows and the algorithms are tweaked.