In the famous counter example for graph isomorphism via Weisfeiler-Lehman (WL) method the following gadget was constructed in this paper by Cai, Furer and Immerman. They construct a graph $X_k = (V_k, E_k)$ given by
$V_k = A_k \cup B_k \cup M_k \\ \text{ where } \\ \quad A_k = \{a_i \mid 1 \leq i \leq k\}, \\ \quad B_k =\{b_i \mid 1 \leq i \leq k\}, \mbox{ and } \\ \quad M_k = \{ m_S \mid S \subseteq \{1,2,\ldots, k\},\ |S| \text{ is even} \}\\ E_k =\{(m_S,a_i) \mid i \in S\} \cup \{(m_S, b_i)\mid i \notin S\}$
One of the lemmas in the paper (lemma 3.1 page 6 ) states that if we color the vertices $a_i$ and $b_i$ with color $i$ then $|Aut(X_k)| = 2^{k-1}$ (color has to be preserved by the automorphism) where each automorphism corresponds to interchanging $a_i$ and $b_i$ for each $i$ in some subsets $S$ of $\{1,2,\ldots, k\}$ of even cardinality. They say that the proof is immediate. But I fail to see how even in the case of $k= 2$. In $X_2 \ (a_1, m_{\{1,2\}})$ is an edge but if we have automorphism which interchanges $a_1, b_1$ and $a_2, b_2$ the above edge gets transformed to $(b_1, m_{\{1,2\}})$ which is not an edge. So that should not be an automorphism.
I would like to understand what is my misunderstanding.