Dnd 5e Magic Missle requires you to be able to see the target. PHB, pg 257 "Each dart hits a creature of your choice that you can see within range."
Therefore you can’t target an invisible creature even if you know the spot they occupy, since you can’t actually see them.
But what if they had an arrow sticking in them? Or a blanket thrown over them. Does that allow the Wizard to "see" the creature in order to use Magic Missle?