how can the geometric realisation of a 1-category have higher homotopical information?
This question hasn't really been addressed so let's talk about it. As Daniël says, this doesn't happen if the $1$-category is a groupoid. You refer to the geometric realization of the nerve as the $\infty$-groupoidification in the title, so I assume you know its universal property: $|N(C)|$, regarded as an $\infty$-groupoid, is the localization of $C$ (regarded as an $\infty$-category) where we invert all of its morphisms. If $C$ is already a groupoid then nothing needs to be inverted so it makes sense that we just get a $1$-groupoid in this case.
So, the higher homotopy must come from having to adjoin inverses of morphisms which are not already invertible in $C$. For every morphism $f : c \to d$ we adjoin a new morphism $f^{-1} : d \to c$ and some coherence $2$-morphisms $f^{-1} \circ f \cong \text{id}_d, f \circ f^{-1} \cong \text{id}_d$ witnessing the fact that $f^{-1}$ is an inverse of $f$, satisfying some coherences (the triangle identities) up to some higher coherences, etc. These coherences must be where the higher homotopy is coming from, so it must be the case that we can in general find some composite of higher coherences which is not required to be trivial.
So let's use Eric Wofsey's very nice example of that $6$-element poset $P$ whose geometric realization $|N(P)|$ is (homotopy equivalent to) $S^2$, which I think must be a minimal example. The image you gave is really nice because you can really see the $2$-cell visually; let's try to see it in terms of coherences. Since there is a unique morphism in $P$ between any two objects I will just name that morphism using the name of the two objects, e.g. the unique morphism from $a$ to $e$ I will name $\overrightarrow{ae}$. So, observe that in the geometric realization we have two paths
$$\overrightarrow{af} \overrightarrow{ae}^{-1}, \overrightarrow{bf}\overrightarrow{be}^{-1} : e \to f$$
from the "north pole" to the "south pole," and these paths are homotopic ($S^2$ is simply connected) but there are two different homotopies between them, one of which goes "east" through $c$ (which involves writing $\overrightarrow{ae} = \overrightarrow{ce} \overrightarrow{ac}$ and $\overrightarrow{af} = \overrightarrow{cf} \overrightarrow{ac}$, then taking inverses, then applying an inverse coherence to $\overrightarrow{ac} \overrightarrow{ac}^{-1}$) and the other of which goes "west" through $d$ (similarly).
Having freely adjoined inverse coherences, there is no reason these two homotopies should themselves be homotopic! And the difference between them (traveling all the way around the "equator") ought to be a generator of $\pi_2(S^2)$. Of course I haven't proven this but you were asking a question about intuition and hopefully it is more intuitively plausible now.