The reprehensible aspect of stealing isn't necessarily that an object has been removed from someone's possession. That may define it from acts of simply taking something, using it, and returning it to the original owner without them noticing, but more generally I would argue that what people dislike about stealing is that someone has claimed a right to own something when they do not have that right. Stealing is more than using something without permission (as this implies that permission might be given when asked); it is an act of someone saying that they themselves have the right to own something when, in fact, they don't.
I don't think that anyone here would claim that the man who lost the prototype isn't, in some part, responsible for what has happened. He made a very, very stupid mistake which he will probably regret for some time. Moreover, it is difficult to consider taking the lost prototype as stealing because it doesn't seem possible to remove an item from someone's possession when that item isn't in their possession in the first place. Nevertheless, I'd say that this act is still disagreeable because the person who has taken the prototype is claiming a right to own it which he simply doesn't have: it isn't his to have.