Harley, who has been loaned back to Exeter until the end of the season, signed for Championship side Swansea last week.
But the Grecians had come in for some criticism for allowing their biggest asset to leave for nothing amid interest from other clubs.
But City`s sporting director Julian Tagg denied reports saying the club turned down a substantial bid for the player.
He told the South Wales Evening Post: "I can categorically state that is one hundred million per cent nonsense.
"It is totally not the case."