here`s an example the top is what it should look like/ the intentional way the bottom is using the glitch. this is around 0:40-1:00 into the game
YES ! I was looking at this today too after I saw your screenshots where the factories were grayed out.
Under the hood, what was happening is that the gray factories were not producing but accumulating cycles, and then once connected they did spit all the $ accumulated. (which is kind of okay?)
In the new update this won't happen, but unfortunately your designs would need a tweak to work again. It makes me a bit sad because it was a smart approach and I do not like cutting "features" out.
I'll be adding some new to compensate !