Funny, I learned about this rule in February. While I travel internationally regularly, I apparently had never heard of the 90 day policy, so when I went to check in for my flight, Swiss (correctly) wouldn't let me finish checking in / board. They pro-actively rebooked me for the following night's flight and I managed to get a same-day passport the next morning.
My only complaint towards Swiss is that I entered all my passport information weeks before in preparation for the trip (e.g. passport number, issuing country, expiration date) yet there were no warning issued at the time on the website. I can't imagine it would be that difficult to cross-reference this and provide the passenger a warning at the very least! Would save everyone a headache and a few dollars.
In case you're wondering, I was one day late to my ski trip but still arrived ahead of a good storm, so all is well that ends well!