At first I had the same issue with 危ない (dangerous).
I don’t think there’s really a trick but at the same time I don’t think there’s really a possible ambiguity if you think about it: if 少ない were a negative form, what would be the affirmative? Can’t be 小い because that would become 小くない in the negative.
As far as I can tell the only way it would work if is you had an ichidan verb *小る whose negative form would become 小ない, but there’s no such word as far as I know.
So it’s like those な-adjectives or nouns that end in い like 嫌い or 装い, if you see them on their own it can be confusing but in context it should always be clear by the way they’re used that they’re not in fact い-adjectives.