I've seen that sort of thing with
Buffalo nickels. I think 2 factors come into play:
1- Sometimes one or two examples are resubmitted many times because the owner believes the coin grades higher than the stated grade. This happens especially when the higher grade is MUCH more valuable than the next grade down. Unless someone notifies PCGS or NGC that they have cracked open the case and resubmitted, the POP numbers are wrong and potentially overstated.
2- Coupled with this, the reality is that dealers and collectors know, with experience, which specific coins are harder to find than others. So they know intuitively that the scarcer coin will cost more. A great example of this is the 1931-S
Buffalo nickel. The mintage for this coin was only 1,200,000, the second lowest in the series. But the 1931-S was heavily hoarded so that today an MS64 example is only about $150 or so. They are easy to find. The next lowest mintage in the Buffalo series is the 1913-S Type II with a mintage of 1,209,000. So technically, there are fewer examples of the 1931-S, but an MS64 of the 1913-S is worth about $1,800. Collectors of Buffaloes quickly learn how common the 1931-S is and how rare the 1913-S Type II is as they look for suitable examples of each.
So supply and demand decides the price- though I don't know exactly why the example you've given seems askew. My guess would be the higher-priced coin is in higher demand and thus harder to find.