Another thing that makes no sense: Allowing JC Romero to pitch to more RHBs than lefties in 2011.
Another thing that makes no sense: Batting Utley and Howard consecutively so that teams only need 1 LH reliever in late-game situations.
Another thing that makes no sense: Pinch-running Erik Kratz for Ryan Howard after Howard had already gotten to third base.
Another thing that makes no sense: Using Jim Thome to PH against LHP Jeremy Affeldt in extra innings at San Francisco with the go-ahead run on third base and only 1 out. Two RHBs were available, including Polanco, who almost never strikes out against LHPs. Affeldt would have had to pitch to Polanco because he was just brought into the game -- specifically to face Thome. This cost them the game.
Another thing that makes no sense: Pinch-hitting for Cliff Lee in the 9th inning of the afternoon loss at LA with 2 outs. Not only was it a poor decision to use Jason Pridie instead of Mike Fontenot, but Lee could have pitched 3 more innings. This mistake cost them the game, as Pridie (not significantly better than Lee at the plate, against RHPs) did nothing, and the bullpen blew the game.
Another thing that makes no sense: Using Michael Schwimer instead of Jonathan Papelbon to come into the game on May 2 at Atlanta with the score 12-9, bases loaded, and only one out. This was obviously the highest leverage situation of the game (and, actually, the season), and Manuel chose SCHWIMER instead of the 50-million dollar reliever. Schwimer allowed all 3 baserunners to score, plus one of his own. This cost them the game.
Another thing that makes no sense: Not firing Radar Map Face before 2013.