The correct completion for the sentence is: "The orders issued by the manager have already been carried out."

• carried over: This implies transferring or postponing something to a later time, which doesn't fit the context of orders already being acted upon.
• carried at: This is not a grammatically correct phrasal verb.
• carried on: This can mean continuing something, but in the context of orders being issued, it doesn't accurately convey the meaning of them being fulfilled or executed.