For me their are only two plot points that ever bothered me:

One was in tEotW with Nynaeve's fantastic tracking ability that seems a bit deus ex machina, which helped partially explain her finding the gang at Baerlon.

The other one is the falcon/hawk/wolf triangle in the second half of Lord of Chaos. This one really feels like a clunky first draft writing of it which is uncommon for this part in the series. Of possible explanation for this is due to the book being waaay behind schedule(him and his editor were in a New York hotel finishing it) and Jordan giving his attention to the other plots of this book that were far more important.