Most probably they were using a Citizen game clock. The top of the line model, The Meijin Sen, can count in various languages, but the older ones that are common (at the Kiin in Tokyo anyway) do not - they beep. The pros that I have seen all use the clock the same way. They have all learned to play purely by sound once byo yomi starts. The beeping all works the same way. Starting at ten seconds the clock beeps five times 10-->6 seconds and then switches to a continuous tone for the last five seconds (beep.. beep.. beep.. beep.. beep.. beeeee.....). The players typically continue reading until the continuous tone starts and then pick up a stone, play it, and press the clock within that final five seconds. They never look at the clock.
The incident makes (some) sense if they were playing like this. In ten-second byo yomi, the clock would never be silent. If Seto had answered Black 169 immediately (during the first five seconds) and pressed the clock, the clock would have simply continued beeping. So it is not hard to imagine that neither player noticed anything at the time. Due to their deep concentration, Matsuoka may not even have felt that the continuous tone started faster than usual, he simply recognized that it was time to make his play, and did so.
The last season or two of the old Tokyo Television (then channel 12) Hayago Championship was played at 10-second byo yomi. It was painful to watch since 10-seconds per play is so much shorter IRL than on the servers. All kind of blunders happened but not the one here since the players still enjoyed the services of a time keeper. The time keepers had a difficult job, though, since they had to count all the time!
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Dave Sigaty"Short-lived are both the praiser and the praised, and rememberer and the remembered..."
- Marcus Aurelius; Meditations, VIII 21