The interrogative word qui always triggers masculine singular agreement. You can see it as lacking number and gender features, and thus agreement defaults to the least marked number and gender: "Je vois que tu as eu peu de visiteurs, qui est venu ?" (even though you know there's been several visitors, the verb is still singular)
The relative pronoun qui however, can trigger all sorts of agreement, because it carries its antecedent's gender and number features to the relative clause: "je ne connaissais pas les femmes qui sont venues"
So you need to be able to recognise which qui you're dealing with if you want your verb to behave correctly. Indirect questions like "je ne sais pas qui est venu" are a trap in this respect, since they look superficially similar to relative clauses, but aren't.