Que

These are just two different ways of forming questions. Either is correct.

Yes, I think "que" is an exception.

This lesson (and the associated lesson for the present tense) describes what's known as "complex inversion", where you put the noun first, then use an additional pronoun for the inversion. With "simple inversion" you just invert the noun and verb. The lesson seems to imply that you always have to use complex inversion with nouns, but I believe this is an oversimplification - it actually depends on what the question word is, and various other aspects of the sentence.

In particular, with "que" you can only use simple inversion.

Thanks for all your answers. Alan, yours was especially helpful. Though Chris commented that either is fine, "que les hommes ont-ils fait," and "qu'ont fait Les hommes." Is this truly the case? Is one of these wrong (making que an exception), or are they both fine?