The verb always agrees with the subject, which in this case is “the crux” (singular).
“the two trees” is the subject complement. As you note, it sounds odd when the complement does not agree with the subject, and I would try to avoid that by rewording, but it is acceptable if you can’t avoid it for some reason.
- The crux of the problem is the presence of the two trees.
Here, a minor addition of a singular noun makes it sound natural without altering the meaning, and the plural noun is safely tucked away into a prepositional phrase—and more distant from the verb.