firstly, while i may have 95 mods in the game and have not tested with the mod alone, i am sure the bug could still happen, at the very least.
so i was running a test in a custom scenario map made to tweak around, while "i love the bug", i doubt it was there intentionally... i was using the Breeder Reactor what i suspect happens is the custom way the reactor works, it burns the fuel in a invisible reactor or something alike but when it has to output the spent fuel and has no space, it is not scripted to turn off before it outputted the spent fuel.
While i do not understand really what goes on under the hood, i can say that adding an extra entity in between would help! like a 1000 space chest, this would let the spent fuel to be outputted, block the reactor from consuming an other cell and also turn off to prevent infinite spent fuel cell breeding. then when taking the spent cells out of the output, the script would place the remaining ones in the output again until empty.
also if it is possible, having 3 separate outputs for "Nuclear Fuels" mod and "Plutonium Energy" and "Vanilla" might help a bit... but having a internal invisible chest would let the fuel to be taken out and let the reactor turn off and not delete the extra cells. i did discover this by using the fuel in mixed orders and only needed 1 cell in the output but it does the same thing with 50 (full stack) of the same fuel being burnt.
