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Our organism gets only the O2 and leaves out all the other unwanted substances.
Not true. Read Decompression sickness. All the gasses are dissolved in your blood. Also, if our lungs only extracted O2, carbon monoxide would be harmless.
But now, if you're there with a cloud of CO2 then you're gonna inhale pure co2 and the mass of co2 will move the o2 gas away, meaning you'll breathe something you can't use. That's why it's dangerous to breathe, not because it'll kill you
Also not true, othewise, CO2 scrubbers would not be required on occupied spacecraft. It will kill you if the concentration is above 8% even if the other 92% is pure O2.