There are many experiments that prepare quantum systems in superpositions of different energy levels. For example, it is common to prepare cavities in coherent states, which are superpositions of SHO eigenstates.
One thing I know about physics is that energy is conserved. That means that if I start with a system in its ground state $E_0=0$ and want to evolve it to a superposition of states with energies $E_0$ and $E_1$, the additional energy must come from the environment, ie the rest of the universe. If before the evolution the rest of the universe had energy $E$, after the evolution I should be in a superposition of $E_0$ in the system and $E$ in the rest of the universe, and $E_1$ in the system and $E-E_1$ in the rest of the universe. Then the state of the system is entangled with the rest of the universe, and the system itself is in a mixed state rather than a superposition.
Clearly this reasoning is somehow incorrect, so what is the loophole that allows us to actually prepare superpositions instead of mixed states?