Let $G$ be a connected graph on $n$ vertices and $1 \le k \le n-1$ an integer. The $k$-token graph of $G$ is the graph $F_k(G)$ whose vertices are all the $k$-subsets of vertices of $G$, two of which are adjacent whenever their symmetric difference is an edge of $G$. Every automorphism of $G$ induces an automorphism of $F_k(G)$ in a natural way. Suppose that $S:=\{x,y\}$ is a cut set of $G$, such that $x$ and $y$ have the same neighbours in $G\setminus \{x,y\}$. In this paper we show that there exist a large number of automorphisms of $F_k(G)$ defined by $S$ that are not induced by automorphisms of $G$. We also describe the group produced by all such $2$-cuts of $G$.