There is a discussion about how much of various gases are necessary for humans to survive in Stephen H. Dole Habitable Planets for Man, 1964.
https://www.rand.org/content/dam/rand/pubs/commercial_books/2007/RAND_CB179-1.pdf
On pages 13 to 19 Dole discusses atmospheric composition and pressure. Table 2 on page 16, table 3 on page 18, and table 4 on page 21 give upper and/or lower limits for various gases.
And of course research in the last 60 years might have modified those limits.
And there are no doubt many thousands of other compounds found in nature or synthisized by chemists which are gaseous at normal Earthlike temperatures.
In the Harry Turtledove story "The Road Not Taken", Analog, November 1985, a Roxlani ship lands in Los Angles. And when the hatches open, the Roxlani find that polluted Earth (or Los Angles at least) air smells bad, while the humans find the air from the ship smells bad (though the Roxlani were unable to keep the ship's air smelling like their homeworld which might have smelled better to humans).
Anyway, mutually bad smelling air is pefectly possible.
You want to select gases which are relatively plausible to naturally occur in a planet's atmosphere, so that the native planet of the species that created the galaxtic standard atmosphere has that gas in its atmosphere and that species evolved with that gas.
If that gas has a detectable oder, they might be used to that odor and not really notice it until it is gone. That gas's odor might mask the sents of other gases on their world, and so they might be troubled by the odors of those other gases which are more common in naturally occurring atmospheres. Thus they make sure to artifically put that gas in the atmosphere of all planets they terraform, even though lifeforms that evolve on planets without that gas tend to find its odor offensive.
Or possibly that species was civilized for so long before they began to terraform other planets that they are very used to the subconsious odor of some artifical pollutant which they accidentially released into their atmosphere that air feels bad without it, so they terraform all planets to have that pollutant in their atmospheres.
Or maybe the odor which they desire is a combination of the odors of several different chemicals. Possibly most worlds have one or two of those chemicals in their atmospheres, but the home planet of the galactic terraformers was a rare planet with three, four or more chemicals in the atmosphere. Thus they would terraform planets to have all of those scented gases in the atmosphere.
Since Earth has only one of those gases, the combined odors of the other gases are offensive to humasn.
I note that sometimes I notice the smells of various plants in the air. Possibly the home planet of the galactic terraformers has very slight seasons, and plants emit pollen all year long, and so the galactic terraformers had to change the seasonal cycles of planets they terraformed, so that the plants from their homeworld which they planted on terraformed planets could release pollen all year long.
I note that breathing a high concentration of helium makes human voices high pitched, and apparently that concentration of helium is not high enough to suffocate someone. So I can imagine that if an Earthlike planet somehow manages to have a high enough concentration of helium in the atmosphere to change people's voices, humans might find that annoying. Since helium is the second lightest gas, and thus would escape very fast from an Earthlike planet, I don't think that a high concentration of helium would be very probable on the home planet of the galactic terraformers.
I note that the surface gravity of a habitable planet has to be low enough for human comfort, while the escape velocity of a planet has to be high enough to retain all the gases for long times - including helium if that is what makes the humans uncomfortable there. There are different formulas for calculating the surface gravity and the escape velocity of a planet.
A planet with a lesser density than Earth could have a surface gravity low enough to be tolerable with an escape velocity which was higher relative to Earth's than the surface gravity was.
I note that Uranus and Neptune both have lots of helium, and even hydrogen, in their atmospheres despite having escape velocities similar to the 11.186 kilometers per second of Earth. Uranus has a surface gravity of 0.886 g, and an escape velocity of 21.3 kilometers per second, 1.904 that of Earth. Neptune has a surface gravity of 1.14 g, and an escape velocity of 23.5 kilometers per second, 2.1008 that of Earth.
But their great distances from the Sun, and thus low temperatures and speeds of particles in their uppr atospheres, help them to retain hydrogen and helium. If they were close enough to the Sun to be warm enough for liquid water using life, they might not be able to retain helium.
If you decrease the density of a planet while increasing its mass and volume so it can have a low enough surface gravity for human and a high enough escape velocity to retain helium, it might turn into a water planet with its entire surface covered by tens or hundreds or thousands of kilometers of water, or even turn into a giant planet with no solid surface.
i note that in the Star Trek episode "Amok Time" there are two features of the planet Vulcan which make it uncomfortable for human:
KIRK: It's lovely. I wish the breeze were cooler.
MCCOY: Yeah. Hot as Vulcan. Now I understand what that phrase means.
KIRK: The atmosphere is thinner than Earth.
MCCOY: In this climate? If the heat doesn't get you, the thin air will. You can't do it!
MCCOY: Is this Vulcan chivalry? The air's too hot and thin for Kirk. He's not used to it.
http://www.chakoteya.net/StarTrek/34.htm
So the temperature and the thin air combine to make exertion on Vulcan uncomfortable for humans.
So possibly galactic standard terraformed worlds have higher or lower temperatures than most Earth humans are comforatble with, as well as slightly different atmosphere, and together they combine to make galactic standard planets rather uncomfortable for humans.
However, I want the “galactic standard” to have a high oxygen content to be conducive to larger creatures and more frequent fires, so just giving humans altitude sickness is not an option (even though it would be the easiest solution).
So maybe your galactic standard planets give Earth humans reverse altitute sickness
which happens when people from high altitudes move to lower altitudes or sea level.
http://yaccatravels.com/blog/reverse-altitude-sickness-symptoms-cure-prevention-and-more
https://www.newscientist.com/lastword/mg24732983-000-is-there-such-thing-as-reverse-altitude-sickness/
The average atmospheric pressure at sea level is defined by the International Standard Atmosphere as 101325 pascals (760.00 Torr; 14.6959 psi; 760.00 mmHg).
https://en.wikipedia.org/wiki/Atmosphere_of_Earth#Pressure_and_thickness
760 mmHg is 760 millimeters of Mercury. According to Dole on page 15, the sea level pressure of oxygen is 149 millimeters of mercury (mmHg). The accepted limit of oxygen for patients who needed extra oxygen was 40 percent of the total atmosphere then, though many persons could & can tolerate higher levels. Dole set an upper oxygen limit that would be tolerable for at least some if not necessarily all humans.
Following this philosophy, for our purposes we may state that the imspired partial pressure of oxygen must be greater than about 60 millimeters of mercury but less than about 400 millimeters of mercury.
https://www.rand.org/content/dam/rand/pubs/commercial_books/2007/RAND_CB179-1.pdf
So if the oxygen content of the atmosphere is close to about 400 mmHg, some people should have problems breathing that much oxygen.
And many other other known gases, especially those which are common on Earth or other planets, have been tested to find upper limits of pressure tolerable for humans. Thus your galactic standard planet could have a higher than Earth normal concentration of nitgrogen, for example, as well as a higher than Earth normal concentration of oxygen, and humans might find breathing such dense air at least slightly uncomfortable, some humans more than others.
On page 20 Dole mentions upper limits for the concentration of dust particles in the atmosphere. However, I can't think of any reason why aliens would find lower concentrations of dust in Earth's atmosphere annoying. But possibly galactic standard worlds have so much pollen in the air (suggested above) that it would be irritatiing or harmful to humans, while aliens enjoy the scent of the pollen and miss it on Earth.
And possibly a combination of various atmosphere factors mentioned in my answer and other answers could make a galactic standard atmosphere more or less irritating to most humans and harmful to some, and make Earth's atmosphere uncomfortable for the aliens for reverse reasons.
