I would like a non-native speaker to weigh in, but I gloss it as "there are ONLY a few and this is ONE OF them" and have never found that confusing or contradictory.
That's exactly the difference: "one of the few" necessarily implies scarcity, whereas you could say e.g. "one of the only grains of sand at the beach" while clearly there are many.
I wouldn’t use that phase for sand grains exactly because there are so many. If you added a qualification like “… that is colored blue” then it sounds fine again to me.
as a nonnative fluent speaker, to me "one of the few" and "one of the only" mean the same thing, with "of the only" possibly being even less than "of the few"
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