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A goalkeeping error from Ben Hamer sent Charlton tumbling to a second consecutive Championship defeat on Saturday.
The Addicks No.1 failed to gather a 72nd-minute corner and Lukas Jutkiewicz pounced to head the winner for Middlesbrough.
Danny Green had gone close for Charlton in a first-half of few chances while he also forced a save from Boro keeper Jason Steele after the break.
There were opportunities for Green and Dale Stephens after Jutkiewicz’s goal but Charlton couldn’t find a way back into the game.
Chris Powell’s side, who also lost their opening game at Bournemouth, go in search of their first league point at Barnsley this weekend.