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I don't have a C3 subscription (yet), so there is limited testing I can do with your game since it far exceeds the free limits. But the main problem I see is that you are checking for collisions between the explosion and Enemies family - and each enemy is made up of two parts, a blank sprite and an animation sprite. Both of those are part of the family and collide with the explosion, so the score gets incremented twice for what is supposed to be one kill...
with the brains, you are only checking for collisions with each of the empty sprites, so that is working the way you expect.