In this Letter, we discuss problems that can arise in the interpretation of results obtained by quantum dynamical simulations with the multi-configuration time-dependent Hartree-Fock (MCTDHF) method. In particular, we show that an effect, which can be seen as the time-dependent version of the state averaging known from standard quantum chemistry, can modify the electronic structure as derived from such a simulation. We illustrate our findings with numerical calculations for the laser excitation of a water molecule, with a Gaussian Type Orbital basis set. (C) 2008 Elsevier B.V. All rights reserved.