I found out a solution for it:

In order to bypass this bug, when you making a conclusions of intuitions, don't mix all of them, but a specific amount of them, depending on how much greater the number of intuitions the game shows you.



It seems like the "Scientific Method" achievement will work out only with 33 intuitions on counter, so the greater number just don't satisfy a condition of an achievement's trigger, though it's work fine for the "Shy" achievement's trigger for some reason. So all you need just stop making intuition conclusions when your counter get a value of 33. To make it easy I suggest you to start mixing intuitions at the end of the game, so you can watch an end's stats to learn the value, load the game and mix a missing number of intuitions.

That's it. Good luck.