The sets in mathematical logic

It is well known that intuitive set theory (or naive set theory) is characterized by having paradoxes, e.g. Russell's paradox, Cantor's paradox, etc. To avoid these and any other discovered or undiscovered potential paradoxes, the ZFC axioms impose constraints on the existense of a set. But ZFC set theory is build on mathematical logic, i.e., first-order language. For example, the axiom of extensionality is the wff $\forall A B(\forall x(x\in A\leftrightarrow x\in B)\rightarrow A=B)$. But mathematical logic also uses the concept of sets, e.g. the set of alphabet, the set of variables, the set of formulas, the set of terms, as well as functions and relations that are in essence sets. However, I found these sets are used freely without worrying about the existence or paradoxes that occur in intuitive set theory. That is to say, mathematical logic is using intuitive set theory. So, is there any paradox in mathematical logic? If no, why not? and by what reasoning can we exclude this possibility? This reasoning should not be ZFC (or any other analogue) and should lie beyond current mathematical logic because otherwise, ZFC depends on mathematical logic while mathematical logic depends on ZFC, constituting a circle reasoning. If yes, what we should do? since we cannot tolerate paradoxes in the intuitive set theory, neither should we tolerate paradoxes in mathematical logic, which is considered as the very foundation of the whole mathematics. Of course we have the third answer: We do not know yes or no, until one day a genius found a paradox in the intuitive set theory used at will in mathematical logic and then the entire edifice of math collapse. This problem puzzled me for a long time, and I will appreciate any answer that can dissipate my apprehension, Thanks!