(little as I want to) I assume you are referring to his belief that Emma was encouraging his suit? If so, I don't know that there were very many contrary indications in her behaviour to be found, if he had been looking for them. He had no idea she was promoting his visits to Hartfield because she had plans for him and Harriet, and John Knightley, an impartial observer, warns Emma in Chapter 13 that her manners to Mr Elton appear encouraging. Likewise the Highbury gossips, we learn from one of Miss Bates' monologues, were talking about a possible Emma/Elton match, though interestingly Miss Bates herself did not think it likely. The only possible clue Mr Elton missed that I can see is Emma's attempt to make him cry off from the Westons' dinner because Harriet is ill and can't go. Presumably he takes this as concern for his health or an attempt on her part to remind John Knightley that it would be civil to offer a seat in his carriage, which John does of his own accord immediately after. Mr Elton, on the other hand, gives any number of obvious clues to his true interest - the charade's mention of a ready wit, the fact that he only ever praises Harriet to praise Emma for improving her or painting her so well, his concern over Harriet's sore throat being much less than his concern that Emma catches it - all of this coupled with Mr Knightley's explicit warning to Emma that Mr Elton will not marry imprudently however sentimentally he talks mean that Emma has ignored far more contra-indications to her desired outcome than Mr Elton has. Therefore if this is a trait they share she has it to a much worse degree.