I would like to propose a simple example of a flat surface of genus $3$ with dark points.
This also gives an example in dimension $3$.
It is based on the following simple observation.

Observation. Consider the torus $T^2=\mathbb R^2/\mathbb Z^2$. Suppose that there is a geodesic segment that joins points $(0,0)$ with $(\frac{1}{2},\frac{1}{2})$. Then it passes through one of four points $(\pm \frac{1}{4},\pm\frac{1}{4})$.

Now consider the double ramified cover $S$ of $T^2$ branching at points $(\pm \frac{1}{4},\pm\frac{1}{4})$. Then on $S$ there is no geodesic segment that goes from any of two preimages of the point $(0,0)$ to any of preimages of the point $(\frac{1}{2},\frac{1}{2})$. Indeed if there were such a segment it would project on $T^2$ to a segment that joins $(0,0)$ with $(\frac{1}{2},\frac{1}{2})$. Hence on $S$ it should pass through a branch point, which is forbidden.

Added. One can desribe give an alternative description of this example. Namely, we can take $8$ copies of squares of size $\frac{1}{2}\times \frac{1}{2}$ and glue a surface of genus $3$ from them in such a way, that at each vertex $8$ squars meet.

If you want a 3-dimensional example just multiply this example by $S^1$. But it should be of course possible to construct examples that are not products, using similar idea.