In the context of quantum cosmology and the Wheeler-DeWitt equation, we investigate the possible effects of a non-semiclassical wave function of the Universe on the evolution of the inflationary perturbations. These are associated with the quantum behavior of the homogenous degrees of freedom (in particular the radius of the Universe) in the early stages of the inflationary expansion, which in turn can affect the dynamics of the trans-Planckian modes of the fields present. The existence of a bounce for the homogeneous gravitational wave function is studied. This can lead to an interference between a contracting and an expanding universe and, as a consequence, to the above quantum gravitational effects on the primordial spectra. In the traditional study of the inflationary fluctuations, such effects are neglected and a quasiclassical behavior for the homogeneous inflaton-gravity system is taken.