It's common for pipes, vent caps, and other obstructions to stick out of the house at about the same height as the ledger. If a vent falls at the top of a ledger, cut a notch for it. If the vent falls in the middle of the ledger, remove the vent cap and extend the duct by 1-1/2 inches. Use a hole saw to make a clean circular cut in the ledger, fit the duct through the ledger, and reinstall the vent cap.
If the obstacle is in the path of a joist, you'll have to frame around it, as shown above. Install ledger pieces on either side, taking care that the pieces are at exactly the same height. Install joists on either side of the obstacle, then cut and install a piece of blocking between the joists. Cut a joist to run from the header to the blocking piece.