) But I can also answer your question without knowing which passage you were talking about.Anyway, in general, you can get a decent percentage of the questions wrong and still score 39-40 on the GMAT, yes. You will definitely get more than 3 questions wrong at that scoring level. So, if you hit a really hard passage and get all 3 wrong, that's fine as long as all three really are hard. (You can't know during the test, of course, how hard the questions are. You just have to gauge your decisions based on how hard the questions seem to you in the moment.)
Also, because you will definitely get multiple questions wrong (that's just how the test works!), it is important to be able to recognize when a question is Just Too Hard and to make a guess and move on before you use up a bunch of time and mental energy on this problem. Chances are, you're going to get this one wrong no matter what, so it's better to save that time and mental energy for other problems.
It's also possible that you'd be able to understand enough to answer the main idea question correctly. Or that you feel comfortable with one paragraph but not the other two paragraphs—so you can answer a question that's about the one paragraph that you did understand. That kind of thing. So, even if the passage is really hard, I'd still at least look at the questions. I'd just be more ready and willing to move on if the question also doesn't make sense to me or if the question is asking about a part of the passage that I know I didn't understand.