Let $X$ be a topological space, not necessarily nice, let $R$ be a subspace of $X \times X$, and let $\overline{R}$ be the closure of $R$ in $X \times X$. Then:
- If $R$ is a reflexive binary relation on $X$, then $\overline{R}$ is also a reflexive binary relation on $X$.
- If $R$ is a symmetric binary relation on $X$, then $\overline{R}$ is also a symmetric binary relation on $X$.
On the other hand, the following claim is false:
- If $R$ is an equivalence relation on $X$, then $\overline{R}$ is also an equivalence relation on $X$.
Indeed, we could take $X = \mathbb{R}$ and $$R = \left\{ (x_0, x_1) \in \mathbb{R} \,\middle\vert\, \exists z \in \mathbb{Z} . -\frac{1}{2} \le x_0 - z < \frac{1}{2}, -\frac{1}{2} \le x_1 - z < \frac{1}{2} \right\}$$ in which case $\overline{R}$ fails to be a transitive binary relation. (Note that $X / R$ is indiscrete, so the smallest closed equivalence relation containing $R$ is $X \times X$ itself!)
Of course, this cannot happen if $X$ is either discrete or indiscrete. What I would like to know is this:
Question. What are some necessary or sufficient conditions on $X$ that ensure that the closure of an equivalence relation on $X$ is always an equivalence relation?
This partial answer solves the problem for connected spaces.
Using the idea from the example in the question you can show that if a connected space $X$ has the property that the closure of every equivalence relation on $X$ is an equivalence relation, then $X$ is hyperconnected.
Conversely, every hyperconnected space $X$ satisfies the property since the diagonal is dense in $X \times X$ (so that the closure of every reflexive relation on $X$ is $X \times X$).
Expanding this, for a general space to satisfy the property every open connected subspace must be hyperconnected. This condition is not sufficient, as restricting the example from the question to the set $\mathbb{Q}$ of rationals gives an equivalence relation on a totally disconnected space without isolated points (which has no open connected subspaces) whose closure is not transitive.