Context. The NASA Kepler mission has observed more than 190 000 stars in the constellations of Cygnus and Lyra. Around 4 years of almost continuous ultra high-precision photometry have been obtained reaching a duty cycle higher than 90% for many of these stars. However, almost regular gaps due to nominal operations are present in the light curves on different time scales. Aims: In this paper we want to highlight the impact of those regular gaps in asteroseismic analyses, and we try to find a method that minimizes their effect on the frequency domain. Methods: To do so, we isolate the two main time scales of quasi regular gaps in the data. We then interpolate the gaps and compare the power density spectra of four different stars: two red giants at different stages of their evolution, a young F-type star, and a classical pulsator in the instability strip. Results: The spectra obtained after filling the gaps in the selected solar-like stars show a net reduction in the overall background level, as well as a change in the background parameters. The inferred convective properties could change as much as ~200% in the selected example, introducing a bias in the p-mode frequency of maximum power. When asteroseismic scaling relations are used, this bias can lead to a variation in the surface gravity of 0.05 dex. Finally, the oscillation spectrum in the classical pulsator is cleaner than the original one.