Atom interferometry relies on the separation and recombination of atom wavepackets. When the two paths overlap perfectly at the end of the interferometer, the phase is insensitive to the atomic velocity distribution. Here, we show that, when the separation and recombination is performed using a Raman transition there is a displacement of the atomic wavepacket due to a phase shift during light pulses. Because of the variation of the laser intensity seen by the atoms, there is an imperfect cancellation of these displacements. The observation of a velocity-dependent phase shift on the interferometer is the signature of this effect, which has been modeled. Thanks to the signature we have identified, we are able to compensate for this effect by applying laser power ramps during the interferometer to mitigate intensity variations.