Dogs with those kinds of flat "smushed in" faces are already prone to respiratory problems and constricted breathing because of their facial and cranial anatomy. The symptoms can be the same sorts of things you get with a human whose nasal passages are not able to provide enough airflow- snoring, mouth breathing, etc. An adult human (at least a conscious one) will be able to take steps to compensate for that if necessary, because: NEED AIR! But the condition is problematic in animals and human infants, who don't have the same ability to deal with it effectively or seek assistance if no one's around to help them.
So yeah I would guess it's a combination of the environmental conditions involved in air travel for the little critters, especially if they are making the journey in a travel carrier stowed away in some part of the plane where they cannot be constantly monitored.
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