First, they're double-counting a lot of passengers in Japan. Tokyo subway isn't a single thing, it's a collection of independent companies, so you need to tap out of one station and tap back into another when changing lines. The JP numbers on Wikipedia are the sum of all the separate Shinjuku stations, which would count a lot of transfer passengers twice.

And second, the table is counting Tokyo's metro system but doesn't include Chinese cities' subways. There are no subway-only stations listed even though plenty of them meet the 30 million passengers/year cutoff. But that's not as big an issue as you might think because even the busiest ones are still far smaller than the big Japanese stations - The busiest is Xizhimen with 237,000 passengers per day, which would translate to 87 million per year. Beijing South Station's subway stop gets 211,000/day = 77 Mn/year, so if we added that the rail passengers it would bring the total to 318 million - but most of them would be going to/from the railway station so that's doing the same sort of double counting as I mentioned in the previous point.

Source for Beijing subway passengers: https://xinwen.bjd.com.cn/content/s684153bfe4b0380e186d0b6e....