I'm building a gameplay proof of concept in C3 and ran into a similar issue. In my experiment, there were new circles that were generating additional circles, which would then move to a specific location, and would be destroyed. There would be a few hundred circles (with attached arrays for state) on the screen at a time, and performance would get very bad WAY sooner than I anticipated.
I used the debugger and discovered that I had made a small mistake in my function to create my circles, and that the number of circles being created were being increased by one each time a new circle generator would be created. This resulted in many thousands of circles being created after a short period of time; they were just stacked and therefore "invisible".
I anticipate you are experiencing something similar to this, and that you'll find your issue in the debugger, because now I literally haven't been able to get a frame rate hit, regardless of how long I let the circle generators continue to be created.