Yes. The sentence "怎麼就來了三個人" only focuses on the small number of people by using the adverbial jiù (就). It is unmarked (there is no presupposition encoded in the sentence).
The sentence "怎麼才來了三個人" is counter expectational by using the adverbial cái (才). It is marked (the presupposition is implied by the adverb cái).