The word "isomorphism" is always relative to a particular structure your mathematical objects carry. Sometimes this is obvious from context, but in many cases clarification is needed.
Here's an example to illustrate the core issue: $\mathbb Z$ is isomorphic to $\mathbb Q$ as a set (because there exists a bijection between them, in other words, an isomorphism of sets). But they clearly aren't isomorphic as rings: one is a field and the other isn't. In many cases, there are either special names for specific types of isomorphisms (bijection, homeomorphism, diffeomorphism, etc.), or it's clear from context which structure is meant.
Elliptic curves feature two major kinds of structure: They are algebraic curves with a group structure on them. One source of complication is that neither of these structures has a special word for its isomorphisms, so we have to distinguish by saying "isomorphism of algebraic curves" or "isomorphism of groups" or "isomorphism of abelian varieties" (which combines the two).
The Montgomery curve $M\colon\; y^2=x^3+486662x^2+x$ is not isomorphic to the Edwards curve $E\colon\; x^2 + y^2 = 1 + (121665/121666)x^2y^2$ as an algebraic curve. One simple reason is that $M$ is smooth whereas $E$ has a singular point at infinity — but smoothness is preserved under isomorphism of algebraic curves, so they cannot be isomorphic.
However, the groups of (regular) points on these curves are isomorphic: The isomorphism is given by the birational equivalence between $M$ and $E$. Note that this does not imply that the birational equivalence is an isomorphism of curves! Indeed, there exist plenty of other elliptic curves with a cyclic group of order $2^3\cdot (2^{252}+27742317777372353535851937790883648493)$ on them, and this group is certainly isomorphic to the group of the same order on $E$, but none of those other curves has a reason to be isomorphic as a curve to $E$.