Ok Here is the breakdown of how this possibly happened.
RMT has been marked by STF
RMT Source
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RMT Mule
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Gil Buyer A
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Gil begins to circulate to normal players
When the STF Decides to remove the RMT gil from the system everyone who has been caught in the RMT food chain winds up getting caught up in the crossfire due to the gil itself probably having been tagged for RMT activity and has to be removed. So characters with large ammounts of RMT tagged gil end up under "Suspicious activity" are investigated found innocent and have any gil tagged as RMT cash removed from their persons as sad as it may be.
Is it the perfect solution? No, but I imagine it's how they roll to remove the most gil from the game with the least ammount of inconvience to the players. (A handfull of gil mongers being caught in the crossfire) instead of the entire economy tumbling out of control.