Well, I see no reason why the action of some arbitrary unitary operator should keep a vector in some subspace. A trivial way to see this is to realise that rotations in two dimensions are unitary, and you can certainly rotate the $\hat{\mathbf{x}}$ vector to some combination of $\mathbf{\hat{x}}$ and $\mathbf{\hat{y}}$ using a rotation!
It's very easy to construct an equivalent quantum example of this. A "physical" example of this is neutrino oscillations: neutrinos are created (and detected) as one of their flavour eigenstates ("electron", "muon", or "tau" neutrinos), but these are not eigenstates of the system's Hamiltonian (which are the so-called "mass" eigenstates). Thus, if an "electron" neutrino is created in the sun and travels to the Earth, it evolves unitarily into a superposition of the other states and so you could well say that: $$\hat{U}(t) |\psi_e\rangle = \alpha(t)\, |\psi_e\rangle + \beta(t) \,|\psi_\mu\rangle + \gamma(t) \,|\psi_\tau\rangle.$$
So even though the system was created as a pure "electron" neutrino, since this state was not an eigenstate of the Hamiltonian, it evolved into a superposition of other orthogonal states.
As to the second part of your question, I don't know how such states are created experimentally, but unitary operations are just one of many types of allowed linear operations, but not all quantum operations need to be unitary: the most notable example being measurements, which cause the wavefunction to collapse to some eigenstate of the observable being measured, and which are certainly not unitary! Only symmetry operations need to be unitary (or anti-unitary, see Wigner's theorem) in order to conserve probability.