The story
From the names of certain species of bird, such as the lesser spotted woodpecker, and the humorous idea that, on account of the complicated name, these species must be rare or obscure. In such names, "lesser spotted" means that the bird has a spotted plumage, and that it is smaller ("lesser") than others of its kind. The popular idea that "lesser spotted" means "seen (spotted) less often" is a misunderstanding of the origin of the phrase, or a play on words.
Etymology from Wiktionary, CC BY-SA 4.0.