Though neither of the coaches said so in their postgame press conference, the brewing discontent may actually have started much earlier, during a strange first-quarter incident in which Harbaugh tried to challenge a touchdown he wasn't allowed to challenge. The 49ers coach threw the red flag to see if Detroit's Brandon Pettigrew(notes) had maintained possession of the ball in the end zone. (Replays suggested he had.) The problem was that Harbaugh couldn't ask for a review on the play because all touchdowns are automatically reviewed by the booth. When his challenge flag came out, Harbaugh was penalized 15 yards for an illegal challenge.
That delighted Schwartz, who was caught by television cameras saying something like "know the rules" toward the 49ers bench. It was hardly the calm behavior of a man who would later be aghast at what he perceived was bad sportsmanship from Harbaugh.
Schwartz was pretty pleased with himself, stalking down the sidelines and reveling in Harbaugh's penalty. He definitely yells something toward the 49ers bench and possibly to Harbaugh himself.
Much of the talk about the handshake controversy implores people to choose sides: Harbaugh should tone it down. Schwartz is a bad loser. Harbaugh was childish. No, Schwartz was.
http://sports.yahoo.com/nfl/blog/shutdown_corner/post/Harbaugh-Schwartz-and-the-first-quarter-play-th?urn=nfl-wp9711Watching the game, I saw Schwartz taunting Harbaugh, you can view it yourself at the link. Now, I don't know if this upset Harbaugh or not, but as the article points out, it sure does make Schwartz look like a hypocrite for complaining about the 49ers head coach's behavior..