Not a simple question by any means. I would have to say that yes, uke is sometimes "wrong" in practice, but that it sets a dangerous precedent to label it as such. I define uke being "wrong" if they act in such a way as to endanger their own safety. Falling incorrectly falls into this category. But then again, in some sense, so does the very act of attacking. As for uke "resisting" a technique, because they know what is coming, that also endangers them. Either because someone will power through a technique and overwhealm their resistance, causing them injury, or because their resistance may result in nage changing techniqes, which, if done unexpectedly, can be pretty devastating.
At the same time, I don't think it is a good idea to tell beginners that their ukemi is wrong. Tell them that they can get hurt falling that way, or resisting that way, but don't tell them that the way they are moving is wrong. There is a lot to be learned from newbies about how your technique will look applied to an unsuspecting and untrained attacker, and telling them that they move wrong and need to shape up is denying yourself an opportunity to learn how to -make-them move correctly.