I was thinking that “heir” and “air” would be a better example of the subtlety 
How about caffeine(e before I but no c, or long a sound like weigh)? Possibly in the same category as protein
Now off the topic of i before e, but still on topic about the things they teach kids in school. The sentences that the first letter of each word is supposed to represent something were kinda ridiculous(I think it’s called a rebus, but I could be Mistaken); like Please Excuse My Dear Aunt Sally(in math class) or the one for the Nine planets in the solar system(My Very Excellent Mother Just Smoked Up Nine Pinters…I mean Served Us Nine Pizzas); and the word representing Earth was different every single year they taught me that stupid phrase(In 5th grade, it was eager, 6th was excellent, 7th was exalted, 8th was eloquent and the 9th grade year[hard to believe that my school was still using such tools when I was a freshman] was …dum dum dum…erotic, no lie; But for the teacher’s credibility, he said Mary instead of Mother).
Reminds me of a time in seventh grade when a kid in my class was doing a presentation in science class about Organisms and kept referring to them as Orgasms. Back on the topic, another word that is an exception to the exception could be …um, I can’t think of another one at the moment. And by posting on this subject, I have lost at life