Excellent, thanks! You're talking about this room, right?
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Here's a thing you can do: from the main menu choose Editing Tools, then Level/Prefab Editor. After it loads, hit Esc to bring up the menu and on the right side click the last icon (two houses). In the bottom search box type "factory" and load up factory_lg_02, which is the Shotgun Messiah factory.
Go to that room and float up just a bit. Here are your zombies that popped in from nowhere. They are waiting on the pipes and drop down right next to you. If they appeared to spawn right in your face, then I think SylenThunder's response applies.
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If you toggle on the sleeper volumes you can see that that entire smelter box is a volume. Setting foot into it will make the zombies drop.
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