The definition of a topological manifold $M$ I have is:
$M$ is Hausdorff.
Each point of $M$ has a neighborhood that is homeomorphic to an open subset of $\mathbb{R}^n$.
$M$ is second countable.
That last one confuses me a little since it seems to me the second condition should imply the third.
$\mathbb{R}^n$ is second countable, thus an open subset $S$ of it is also second countable through the base: $B_S = \{U \cap S : U \in B; S \subseteq \mathbb{R}^n\}$ where $B$ is the base of $\mathbb{R}^n$,
In English, grab the base for $\mathbb{R}^n$, for each set in it, intersect it with the open space, append all the results to a new set. By construction this new set is both countable and any open set in $S$ is a union of sets in $B_S$.
And now use the homeomorphism $\phi$ to map the base sets onto $M$, Since we used a homeomorphism the resulting set $\phi(B_S)$ should be a countable base for $M$.
Where is my logic failing? What is an example of a topology that ahs the first 2 properties without the third?
I see three issues with your argument.
In short, nothing about this gives a countable basis for the topology of $M$.