The somewhat intuitive idea of 'holes' all depends on the definition of the word of course. In a much more naive notion of 'holes', $\mathbb{Q}$ doesn't have any, as for any two $p, q \in \mathbb{Q}$ ($p < q$) one can always find another $r \in \mathbb{Q}$ such that $p < r < q$. Of course, it is well-known that $\mathbb{Q}$ is not complete, while $\mathbb{R}$ is. In that sense, $\mathbb{Q}$ does have holes, whereas $\mathbb{R}$ does not.
My question is if there is any sense in which $\mathbb{R}$ does have holes. I know little about 'extensions' of $\mathbb{R}$ (not sure if that's the right term) like the surreal or hyperreal numbers, but as far as I know, those don't fill up any 'gaps' in $\mathbb{R}$, they simply 'add more'. In other words, I am wondering if there is a property that $\mathbb{R}$ (with its standard topology and all that sort of thing) does not have, which could be described as $\mathbb{R}$ having holes (in the sense of that property).