Sometimes leagues will have teams with compensatory picks, or a team that has more than one pick in a round.

To handle this situation, the commissioner will have to step in and utilize an in-draft tool called "Keeper On The Fly". This will allow the commissioner to essentially add a player to a roster at any point in the draft.

Only the commissioner has access to this tool, which is available in the Draft Tools area.
Click on the (...) drop-down and then select "Keeper On the Fly", as per the image below. the team and player. Finally, click the "Add Player to Team" button to finalize.