....I'm gonna have to say that at best we should have phlogistion.* The reason I say "at best" is because the theory was made in the 1600s, but didn't really have any new data that didn't exist for hundreds of years prior. Basically: it was known that fire caused a process by which air gained or lost some property that allowed fire (and other oxidation processes) to work. Eg. "dephlogisticated" air couldn't sustain life, burn wood, or rust metal, no matter how hard you tried.
*Slightly made up word. I couldn't find the proper tense verb form of the word.
If you're saying that there shouldn't be air flow control systems because dwarves don't understand air, you're assuming two things I don't particularly like...
First, you're assuming that dwarf science and technology would progress perfectly along the same lines as human science.
Second, you're assuming that dwarves would have to understand something like a perfect understanding of modern chemistry to be able to do something like set up a ventilation system.
Dwarves live underground. Humans didn't. Creatures that live underground in cramped caves that are filled with numerous breathing creatures are going to notice that air goes bad eventually. Even without advanced understanding of how gasses work in mines, miners were using canaries in the coal mine, after all. Dwarves, who live in far more extreme subterranean conditions, to the point of being entirely capable of having entire cities where few, if any, dwarves ever see the surface for periods as long as perhaps their entire lives, would probably have a much better empirical understanding of how gasses behave in enclosed spaces than the older human idea that air is somehow a void.
Even if they don't know what, exactly, is going on, they can understand when something makes air easier to breathe, if they have access to it. If this were some kind of organism that somehow released oxygen in a non-photosynthetic reaction, and dwarves noticed that it became easier to breathe (and why wouldn't dwarves either use canaries, or just plain adapt to cave life by being sensitive to air quality?) when that sort of strange glowy fungus was around, they would probably start wanting more of it around wherever there were plenty of breathing creatures.
If they can build a fan, if only to move miasma away from them (which they can certainly understand comes from rotting corpses), they can build a fan that moves hard to breathe air away from them. If you want to call it "phlogmatic air" or whatever, instead of something simpler, like "depleted air", then that's little more than an argument of terminology. (I honestly have little taste for such terms, myself, but it's not worth getting too up in arms over.)