I couldn't find my problem noted anywhere so I wanted to bring this up. I have spent a long time trying to figure it out but I eventually came to the conclusion that it probably shouldn't be happening. I have a gas pump which is pumping large quantities of oxygen which I am using a gas filter to filter that out to the dupes. The rest is hydrogen which carries on through the pipeline to my hydrogen generator. From the screenshot below you can see that there is some oxygen that is going in both directions (filtered out and passed by the filter). In actuality more oxygen makes it past my filter and to my hydrogen generator then what actually gets caught by the filter and siphoned out.
My save file is also there.
Hope this helps fix some bugs in an otherwise very fun game.
Built it as seen in picture. Gas filter and hydrogen generator. Then created the gas pipes from start to finish. Added the filter last.