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Even before Gagne through a pitch, it just seemed like a bad idea to put him in (since he has been terrible since going to Boston), and indeed it was. Extra inning 5+ hour games just stretch bullpens to the outer limit.
They can't wear out his arm. That was the longest Papelbon has pitched all season, and any more would have meant he would have to sit out the next couple games. Last week's SI had an article about him, and he has some weird shoulder condition that makes his fastball amazing, but it is really easy for him to tear his rotator cuff.