I was paying attention to when it seemed that something might not be right with the relationship with Willoughby and Marianne. I really think that while the narrator of the story takes on different points of view, the truly omniscient narrator (when not being ironic or making fun) is taking the point of view of Elinor. As someone else wrote, too, I am a big Elinor fan (a fan of "sense" I suppose.) All the information the family finds out about Willoughby - not observed directly - is positive. Sir John shows no reservation about him and indicates he would be a good catch. I guess we can't necessarily rely on Sir John's testimony, but given that gossip travels fast with him and his mother-in-law, and nothing untoward has been reported about him, this is positive enough.
Certainly, Willoughby can be criticized for his judgmentalness of others such as Brandon, but even in Elinor's eyes, that is not something in which to completely disapprove of him, since he shows genuine affection towards his sister, etc. There is nothing in the story to overly suspect anything about Brandon out of the ordinary until Elinor (and again, I think her observation really is the unsatired look of the omniscient narrator) mentions in Ch. 14.
So wondered [regarding the sudden departure of Col. Brandon], so talked Mrs. Jennings; her opinion varying with every fresh conjecture, and all seeming equally probable as they arose. Elinor, though she felt really interested in the welfare of Colonel Brandon, could not bestow all the wonder on his going so suddenly away, which Mrs. Jennings was desirous of her feeling; for besides that the circumstance did not in her opinion justify such lasting amazement or variety of speculation, her wonder was otherwise disposed of. It was engrossed by the extraordinary silence of her sister and Willoughby on the subject, which they must know to be peculiarly interesting to them all. As this silence continued, every day made it appear more strange and more incompatible with the disposition of both. Why they should not openly acknowledge to her mother and herself, what their constant behaviour to each other declared to have taken place, Elinor could not imagine.
Until this statement, I, as a reader, am not particulary alerted to any concern about Willougby and Marianne except that they seem to be rushing into things pretty quickly. I suppose if I were from that time and familiarly understood the propriety involved in behaviour between unmarried or unengaged single young people, I may have suspected earlier, but it isn't a specific point made until this statement regarding Elinor's wonder at Marianne's and Willoughby's silence. Would anyone else find a different place to start becoming a bit worried?