I think this game revolves around the speaking clock.
An error of 1 second could spell the death of a player easily.
The tube can only hold 300 seconds of liquid. Not 301, exactly 300.
Lets say a player wants to fill the tube with 15, 25, and 20 totaling 60 seconds. If the third round he failed and filled the tube for 21 seconds, that means he need another round to round it up or take the penalty to reset. The base penalty is 1 minute, so a player safest play is to total their tube in multiple of a minute. I imagine it's like a blackjack, where you can only push near 21 for so much. Even one point value too many spells your death.
My speculation is, Souichi tried to fill his tube for 6 seconds, to round up his 25 into a thirty. I imagine it's easier to round up that thirty into a sixty because the clock reminds you verbally every 10 second. I imagine the 10 seconds dong is adjusted properly.
However, A clock that reminds you every 10 second may have an error between the 0 to 10. The space between the line in a ruler's mark. Even between the ticks, there's a space you cant pinpoint. What if the seconds are counted not by the ticks, but by the space between the ticks? That would be a mechanical problem that sounds plausible to me. Besides that, The fact that we have two clock, speaking and watch, is already an imperfection waiting to be exploited.
However, If there's anything more perfect than that clock, it's Souichi's biological clock. He's the only one that could spot imperfection between the two clocks.
I already said that souichi tried to round up his 24 to a thirty. Before that, he tried to match Baku's tube to his 24 but made an error of a second. This time around, he made another error of not turning at 6 second to round up his 24 to a thirty. Hence, the mistake implied this chapter. Is not the penalty, but his failure of rounding up his 24 hypothetically cleanly. Souichi is too perfect, His biological clock has been trying to adjust these few rounds.