Well, you're not really doing it "wrong" per se, but the way you have one object sending commands to another object which sends commands to another object makes a sort of sticky web that's hard to untangle.
Re-usability is fine the way you describe it... for one-off things like shooting bullets or making explosions. Yeah you can have the objects take care of that themselves because explosions and bullets are just fire-and-forget kinds of things. The problem of dependencies here is that your fade behavior on your CoreSpark is sending out commands when it should be acting more like an explosion or a bullet. It's a just special effect. But since you have the next sequence of events depending on whether or not CoreSpark has faded away, it's suddenly become an important, center-stage player and without it the whole show stops. The Core should be deciding what happens to the CoreSpark, not the other way around. Or better yet, the Core should just create the CoreSpark, and then forget that it even exists, and just go on to do it's own thing. Let both Core and CoreSpark fend for themselves.
That's the concept of encapsulation. Information is restricted between objects. Each object is doing it's own thing without knowing what the other objects are doing. Your Core doesn't need to know that your CoreSpark is done fading. Therefore, the CoreSpark can safely be removed and there is no adverse effect on the rest of the game.
There were some other examples of things like this going on in your game logic, but I'm not on my Construct computer right now so I can't recall exactly what they were. And like I said, it's not really "wrong," it's just harder to unravel.
Anyway, I still haven't really gotten a chance to take more in-depth look into your .cap yet. I'll let you know when I do. My guess though is that it's going to end up being bugged somehow, so in the mean time if you can try paring it down to just the components necessary to recreate the bug then that would be good. That's all I'll be doing anyway, I can't see what else there is to do.