Let $A = \mathbb{N} \times \mathbb{N}$ and define a relation $R$ on $A$ by $(a, b) R (c, d )$ iff $ab = cd$.
Obviously $R$ is an equivalence relation.
Problem: List the elements in the equivalence class $E_{(9,2)}$.
Modified
$E_{(9,2)} = \{(9,2),(2,9),(1,18),(18,1),(6,3),(3,6)\}$.
Is this correct?
It is not correct. First, elements of the equivalence class of $(9,2)$ are, like $(9,2)$ itself, elements of $A$, not elements of $A\times A$: they are simply ordered pairs of natural numbers. $(9,2)$ and $(2,9)$ are elements of that class; the ordered pairs of ordered pairs that you wrote down are not.
Secondly, you missed four elements: $(1,18),(18,1),(3,6)$, and $(6,3)$. Each of these pairs is in the same class as $(9,2)$, because in each pair the elements have the same product as those of $(9,2)$, namely, $18$.