It emerged ahead of this weekend's season finale that the #17 Real Racing Honda and the #19 Racing Project Bandoh both performed illegal overtakes on the #22 R'Q Motor Sports Mercedes-AMG GT3 in the 10-second countdown period leading up to the FCY period on lap 17 of 65 in the penultimate round of the season.
Both cars escaped penalties, with the Real Honda of Nobuharu Matsushita and Koudai Tsukakoshi going on to score a victory that has kept them in the running for the title this weekend at Motegi.
A spokesperson for the GTA explained during Sunday morning's pre-race press conference that the stewards had failed to notice the overtakes in question until well after the race results had been made official, clarifying that both the #17 and #19 cars should have been penalised.
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He added that the FCY system, which was only introduced in SUPER GT last year, up until now did not provide an in-cockpit warning to GT500 drivers about overtaking a GT300 car, or vice versa.
The system has been updated since the Autopolis race to alert drivers and officials to any overtake performed during the FCY procedure, irrespective of class.
Race director Naoki Hattori is understood to have apologised to the drivers during Friday evening's briefing and reminded them that overtaking is not permitted in the 10 seconds prior to the start of the FCY.
Both the spokesperson and GTA chairman Masaaki Bandoh were keen to reiterate on Sunday morning that the in-car warnings are only to be used as a reference, and that the flags and boards displayed the marshals take precedence in case of any discrepancies.
The spokesperson confirmed that the FCY board - which is shown at the start of the 10-second countdown - was being displayed at the last marshal post before the illegal overtakes occurred at Autopolis.
Real Racing's title chances took a blow in qualifying for the Motegi finale on Saturday as Matsushita could only qualify 10th, while the points-leading Impul and NDDP Racing Nissans start third and fourth respectively.