This is just how I like to run, but I only give Discontent for clues (and clue-level-type secrets) only when it clicks for the players. Like, if you offhandedly mention, "oh, yeah, the football team has no competition" and keep talking, wait for the players to investigate and examine and make the realization before their Discontent starts rising.
Consequences I like to add closer to the "finale," when players have a lot of secrets and are close to figuring the whole thing out. Think about, like, a Twilight Zone episode, of how things really start to go awry only as the protagonists get more and more involved in the problem.
But, critically, both of these are just how I, Sam, run. Other people—even my co-designers—will run the game differently. It's rules-light for a reason: do what you think is best!