In this particular case, Stalker Points have a flaw because SAO was not available on Amazon for about a month or so after it was first solicited due to the Amazon dispute. Not knowing how long the dispute would last, some people may have already pre-ordered at other stores and thus won't be counted at Amazon. Eventually the dispute was actually resolved, and Amazon pre-orders (and thus, Stalker Points) picked up again, but we have no idea how many people already pre-ordered elsewhere and how that will bias the rankings.
Basically, Stalker Points depends on Amazon being representative of the entire market. Any time when it isn't for various reasons, it risks being unreliable. They've tried to improve the algorithm over time to accommodate for discrepancies observed, but unexpected things do happen from time-to-time.
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