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Looking at the MO reputation league I found that it shows up 1767 screens, all screns but the last one show up 9x4=36 users and the last screen shows 27 users. So totally MO has 1766x36+27=63 603 users.

On the other hand, in the profile of the MO leader Hamkins we can find that he is 0,02% overall. But if MO indeed has 63603 users, he should be $\frac1{63 603}\cdot 100\%\approx 0.0017\%$ overall.

The same problem with other users:

for David Speyer is written 0,04% but should be $\frac2{63 603}\cdot 100\%\approx 0,003\%$

for Joseph O'Rourke is written 0,07% but should be 0,005%

for Qiaochu Yuan is written 0,09% but should be 0,006%,

and so on...

What is the reason in such more than 10 times difference?

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If you click on the number "0.0x%", the links gets you to reputation league for MathOverflow. (The link given in the question is actually list of the registered users and not the reputation league.)

As far as I know, only users from reputation leagues count for the purpose of these statistics. (That means that cut-off is at 200 reputation points. Notice the explanation in the sidebar: "users with less than 200 reputation are not tracked in the leagues". It is, at least to some extent, reasonable. Probably we don't want to count the users who never interacted with the site, just created an account. Which means that any reasonable cut-off should be above 101 points.)

Currently there are 4456 users in the reputation league. Considering that the the percentile is taken from these users, the numbers seem about right: \begin{align*} \frac1{4456} &\doteq 0.022\%\\ \frac2{4456} &\doteq 0.045\%\\ \frac3{4456} &\doteq 0.067\%\\ \frac4{4456} &\doteq 0.090\% \end{align*}

See also:

I will also add that unregistered users are counted in reputation leagues (if they have at least 200 reputation points) but they are not shown in the list of users. Existence of unregistered users also explains why you counted approximately 64k users while official stats show 74k users. (The latter includes the unregistered users.)

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