It took me a while to get the ball spawners and nearby effects working properly even though there is a prefab for it. You have to make sure you have the proper filters set up for the physics_trap and the vphysics_motion, or you will not get what you expect. This can be partly done from the spawnflags of these entities. But if you want one of the triggers to include or exclude a single entity type (such as combine_ball) you need to set up a filter_activator_class and target it in with the filtername key of the physics_trap or vphysics_motion. Note that the prefab, if you have copied it, does NOT include the filter entity even though the filtername key of the triggers targets one.
One more thing: the prefab for the ball spawner it set up so that all the effects (beam, sound, spawner, and the 2 triggers) start off. This I assume is so that you can turn it ON 1 second or so after the map starts (with a logic_auto), that way there is less chance of bugs arising from unspawned entities, etc.