
This seems a bit like distinctions we make in other areas of language use. For example, politician and statesman have the same denotation (they refer to the same person) but a different connotation (statesman is more positive). Similarly, eat and dine have the same denotation (they refer to the same activity) but a different connotation (dine sounds rather posher). And maybe this is similar to the distinction between frog and toad ― they refer to the same creature, but toad has a more negative connotation.
Or perhaps it is just a case where scientific taxonomy and everyday linguistic usage diverge. In popular usage, frog and toad seem to refer to quite different animals, even though scientific evidence does not confirm this distinction.