Where the indiscrete topology was used (in the counterexample)?
Let $(X,\tau)$ be a topological space. If $X$ has the Bolzano-Weierstrass property then $X$ is compact.
Counterexample
Let $Y$ consist of two points; give $Y$ the topology consisting of $Y$ and the empty set. Then the space $X = \mathbb{Z}_{+} \times Y$ is limit point compact, for every nonempty subset of $X$ has a limit point. It is not compact, for the covering of $X$ by the open set $U_n = \{n\} \times Y$ has not finite collection covering $X.$
It is used in the highlighted portion.
That is true only because in Y, every point is a limit point because it has the indiscrete topology.
Let the points of Y be named $y_1$ and $y_2$. For any point $z=(n, y_1)\in X$, any neighborhood of $z$ must also contain the point $(n, y_2)$ (and vice versa). So every point of $X$ is a limit point. Note that the author has used the product space notation for X, I.e., the author is using the topology on $X$ which is a product of the discrete topology of $\mathbb{Z}_+$ and whatever topology is put on $Y$.
As to what happens if Y did not have the indiscrete topology... there are only 3 other possible topologies - the discrete topology and the two Sierpiński topologies. In all those cases, you can find a singleton set that is open in X and it is no longer true to say “every nonempty subset of $X$ has a limit point”.