We observe that a multi-conjugate adaptive optics (MCAO) system produces rapid fluctuations of irradiance of a few percent in the compensated focal plane when observing an extended target, such as the solar surface. Such fluctuations are absent in the uncompensated focal plane. The fluctuations are apparently correlated with the local curvature of deformable mirror in the plane conjugated to the high altitude turbulence layer. They can be explained by the field dependent change of effective focal length introduced by a high altitude turbulence layer, which is related to image distortion. Using a simple geometric model of the MCAO system, we are able to reproduce the observed irradiance effects. We propose to introduce a slightly undersized aperture stop at the location of the nominal exit pupil in order to remove the fluctuations in the compensated field.