Hey Jean - thanks for the quick reply!
I have several "traps" in my scene that the player must negotiate through, most of which are prefab objects that stay in the scene but they're not creating anything, I'm just activating pieces collision triggers and FX.
However, I do have a fireball launcher that shoots a sphere up into the air and a few seconds later the sphere is destroyed. I've attached a screenshot to show you how I've got it setup. The short version is - an empty game object loads a prefab sphere, the sphere spawns in and launches itself up into the air, and then a few seconds later destroys itself.
As for additive scenes, I don't think I'm doing that, though that would explain why I load scenes between my main game level I don't see the numbers reset to where they started from. I went through all of the FSM's where I'm calling Load Level and I don't have additive checked. Is there somewhere else that additive could be set?
Thanks a ton for the help!