The effect of electron-vibration interaction in atomic-scale junctions with a single conduction channel was widely investigated both theoretically and experimentally. However, the more general case of junctions with several conduction channels has received very little attention. Here we study electron-vibration interaction in multichannel molecular junctions, formed by introduction of either benzene or carbon dioxide between platinum electrodes. By combining shot noise and differential conductance measurements, we analyze the effect of vibration activation on conductance in view of the distribution of conduction channels. Based on the shift of vibration energy while the junction is stretched, we identify vibration modes with transverse and longitudinal symmetry. The detection of different vibration modes is ascribed to efficient vibration coupling to different conduction channels according to symmetry considerations. While most of our observations can be explained in view of the theoretical models for a single conduction channel, the appearance of conductance enhancement, induced by electron-vibration interaction, at high conductance values indicates either unexpected high electron-vibration coupling or interchannel scattering.