Threads have popped up on the Call of Duty website, Reddit, Steampowered, and 4chan's /v/ board about this issue.
A support member from Activision replied to the Steampowered thread with the following information for affected users.
We do need some of your help in order to find out what's going on. If purchased Call of Duty Black Ops II and you did receive a copy of Mass Effect 2 with your physical copy of the game, let us know where you purchased the game from. When you purchased the game and if you can provide a city and state to where you purchased the game from. This will help us go a long way to find out what's going on.
We know that you want to play the game as soon as possible and luckily you can. I know most users on the Steam forums have a Steam account but for those people who find this through Google or Bing, here are the instruction on how to add a game to your Steam Library. Make sure that you have a current Steam account or create a steam account.
Please follow these instructions to activate a new retail purchase on Steam:
Launch Steam and log into your Steam account.
Click the Games Menu.
Choose Activate a Product on Steam...
Follow the onscreen instructions to complete the process.
This is actually the first oddball mistake made today concerning retail discs for newly released games.