Suppose we use Tarski-Grothendieck set theory as a foundation for category theory (ZFC together with the assumption that every set is contained in a Grothendieck universe, or equivalently that there is a proper class of inaccessible cardinals). It is sometimes necessary when working in this theory to pass to a larger Grothendieck universe. However, given Grothendieck universes $\mathscr U\subseteq\mathscr U'$, it is possible that $\mathscr U$ is not an elementary substructure of $\mathscr U'$: there exists a formula $\phi(x_1,\dots,x_n)$ in the language of set theory with parameters $x_1,\dots,x_n\in\mathscr U$ such that $\phi^{\mathscr U}(x_1,\dots,x_n)\leftrightarrow \phi^{\mathscr U'}(x_1,\dots,x_n)$ does not hold. For example, if $\mathscr U$ is the smallest Grothendieck universe, and $\mathscr U'$ is the second smallest, then $\mathscr U$ thinks that Grothendieck universes do not exist, whereas $\mathscr U'$ thinks that exactly one Grothendieck universe exists.
Question. Does this "lack of agreement" between Grothendieck universes ever present problems in category theory?
Some thoughts
One could "fix" this problem by assuming something stronger than Tarski-Grothendieck set theory. For example, one could postulate that there is a proper class $I$ of inaccessibles $\kappa$ such that $V_{\kappa}$ is an elementary submodel of $V$. This idea is presented in the following answer by Joel David Hamkins. (Postulating this within the framework of ZFC takes a little work, due to complications relating to Tarski's theorem on the undefinability of truth, but it can be done.)
However, for most "down to earth" category theory, using a stronger foundation than Tarski-Grothendieck set theory seems unnecessary. To take an example, suppose $\mathscr U$ is a universe, and $\mathcal C$ is a category such that $\DeclareMathOperator{\Hom}{Hom}\Hom_{\mathcal C}(X,Y)$ is isomorphic to an element of $\mathscr U$ for all objects $X$ and $Y$ in $\mathcal C$. Consider the question of whether a functor $F$ from $\mathcal C^{\mathsf{op}}$ to the category of $\mathscr U$-sets is representable. This question does not depend on the choice of $\mathscr U$, in the following sense: given any universe $\mathscr U'$ such that $\mathscr U\subseteq\mathscr U'$, the functor $F$ is representable if and only if $F$ is representable when viewed as a functor into the category of $\mathscr U'$-sets. More generally, I believe the paper Universes for category theory by Zhen Lin shows that a number of universal constructions are not "universe dependent".