Let $\hat{H}$ be a system of lattice fermions with two internal states per site, so they can be described using operators $\hat{c}_{m,\alpha}$, with $m$ denoting the lattice site and $\alpha$ the internal state. An anti-unitary operator $\hat{U}$ acts on these operators as $$\hat{U}\hat c_{m\alpha}\hat{U}^{-1}=\sum_\beta\mathcal U_{\alpha\beta}\hat{c}_{m,\beta}.$$ Since $\hat{U}$ is anti-unitary, it also satisfies that it acts over imaginary scalars as $$\hat{U}i\hat{U}^{-1}=-i.$$
Now suppose that at time $t=0$ I have a state $|\psi(0)\rangle$that is invariant under this transformation, $\hat{U}|\psi(0)\rangle=|\psi(0)\rangle$. Now, I evolve the state with a second-quantized Hamiltonian $\hat{H}=\sum_{m,n,\alpha,\beta}\hat{c}_{m\alpha}^\dagger H_{m\alpha,n\beta}\hat{c}_{n\beta}$ that is symmetric under the transformation $\hat{U}$, i.e. $\left[\hat{H},\,\hat{U}\right]=0$. Then I have $$\hat{U}|\psi(t)\rangle=\hat{U}e^{-i\hat{H}t}|\psi(0)\rangle=\hat{U}e^{-i\hat{H}t}\hat{U}^{-1}\hat{U}|\psi(0)\rangle=e^{+i\hat{H}t}|\psi(0)\rangle\neq|\psi(t)\rangle.$$
Therefore, even though both the initial state and the Hamiltonian are invariant under this transformation, the anti-unitary character makes that any evolved state will break that symmetry. However, this is conceptually a bit strange for me, especially for anti-unitary transformations that have nothing to do with time or time-reversal (for example, sub-lattice symmetry). Since these transformations are used e.g. to classify topological insulators, how can it be that a mere time evolution breaks the symmetry? This has no counterpart for unitary transformations and I don't really get the conceptual meaning of this fact.