In a homework set I am assigned there are three structures we need to prove are not manifolds; the space of square matrices with $0$ determinant, the space of quintic polynomials with three real solutions, and two intersecting lines in the plane.
Let's look at the last one. It's well known. The argument is outlined in Tu's book: if $U$ is any neighborhood of the point $p$ at which the lines intersect then the property that a manifold is locally euclidean of dimension $n$ leads to a contradiction, because the number of connected components is not preserved.
But a classmate brought up a good question that stumped the graduate TA as well as me; when proving a space is not a manifold, are we proving that a topological space is not a manifold? Or that some underlying set is not a manifold when given any atlas, or any topological structure? After all, it was noted that $\mathbb{R}$ with the indiscrete topology $\{\mathbb{R}, \varnothing\}$ is not a manifold.
So how do we know that any open set containing the point of intersection for the cross necessarily contains points near that point, and thus the lines? This assumes that the open set has the form of an open set in the topology inherited from $\mathbb{R}^2$, but this is not made explicitly clear anywhere.