The changes in collision masks when SE is also installed break the Selection priority for the Vehicle Depot from AAI, to fix this a patch has to be added that changes the selection priority of the different vehicle depot entitles when both mods are installed to ensure the right entity (the container and maybe the signal) can be selected.
Can't think of a generic way to fix this so I guess a fix would have to be added for every multi entity that breaks due to collision mask/selection priority problems.