Thomas Paine understood the problem.

He that would make his own liberty secure must guard even his enemy from oppression; for if he violates this duty he establishes a precedent that will reach to himself.

Karl Popper's philosophy calls for directly and actively suppressing the people you and I deem "intolerant". The fundamental problem with his philosophy is that the Nazis are already in charge. Any method you use to suppress "the intolerant", you give to the Nazis. It goes straight into their hands for them to use against the people they deem "intolerant". Popper asks you to forge the tools of your own demise.

Thomas Paine's philosophy breaks the cycle. He opposes fascism in general. When you instill Thomas Paine's values in the general populace, you discredit yourself in their eyes as soon as you call for suppressing anyone.

Fascism that you happen to agree with is still fascism. Popper's actual paradox is that he was a fascist.