Explanation (taken straight from my post in one of the weekly charts threads):
The 31st, the 3DS had shipped 18.7 million to japan (Nintendo's own words). At that time it had sold 18 million in Japan (we know this is correct because of Media Create and Famitsu). That means there were 700k on shelves, just in Japan. The problem about that, is that VGC says the 3DS had 300k on shelves at that time. For the entire world. And I'm sure you all understand that that is 100% impossible.
There you go. Even if there were not a single 3DS on shelves in the entire world except what we know is in Japan, it still has 700k on shelves. If we are going to be realistic, it also has at the very least 300k in both Europe and America, so there should be 1,3 million on shelves. That leaves us with an overtrack of 1 million.
Sources:
Nintendo Investor Relations: http://www.nintendo.co.jp/ir/pdf/2015/150128e.pdf (final page)
Media Create + Famitsu.
EDIT, as per may 7th; we now know 3DS ltd shipments are at 52.06 million as of the quarter ending 31st march, which means that according to VGC it has sold ~150k more than it has shipped. Realistically, the 3DS is probably around 51 million now, not 52 million, and this could be seen from last q numbers as well.









