Broken Steel bugs

Unable to get up at Wake up after two weeks

 * Finished the main game starting the Purifier with the main character. After the ending movie, Lone Wanderer woke up at the Citadel, unable to move. None of the console commands worked.
 * This might help: let Sarah start the Purifier. Once she entered the Purifier, game gave a quest end confirmation "secure the control room". It never came while trying to start the Purifier as Lone Wanderer or sending in Fawkes.
 * This can also happen if you send any character into the purifier control room, even yourself. There are a couple possible causes like having weapons and armor you are not supposed to, or using a non-standard class. There is a 3rd party fix for if you are using a non-standard class which can be found at Fallout Nexus here. It is unverified if it works on other causes for this problem.

Unable to complete quest

 * After speaking to Elder Lyons about the events of the past two weeks, he directs you to Scribe Rothchild. After asking Rothchild for an update on the situation, he tells you to follow him to the map, but he fails to lead you there, instead carrying on with his daily routine.
 * A way to fix this is talking to Rothchild repeatedly (pushing 'E' nonstop), and pushing him towards the map (i.e. walking into him), then enter console and type and follow him until he finishes talking. Enter conversation and hey presto the game goes on! (Note this only works if you're both in the Citadel Labratory).
 * Similar to the above bug, once Broken Steel is completed with the 'good' ending and your Vertibird lands back in the Citadel courtyard for Lyons' speech, the speech never occurs. Your character is locked into the 'listening' pose but Lyons, Rothchild, and Sarah simply walk off and continue their daily routine leaving you stuck there. This makes the good ending impossible to finish, effectively defaulting you to blowing up the Citadel, as doing so does not involve a speech at the end.
 * Fix for this issue: After the game loads the Citadel and you are stuck at this screen, open the console via the tilde "~" key and type . This should give you control over your character, and then you can run to Elder Lyons and talk to him, thus completing the quest.
 * After the Purifer is activated, the normal ending cutscene plays, but returns to the player stuck lying on the ground and unable to move. (Replicated at least twice.) 2 identified causes are that you are using a non-standard class or are in possession of an object the player is not supposed to be in possession of (i.e. the non-degrading Gauss rifle from inside the Anchorage simulation).
 * This can be fixed through a 3rd party mod found at Fallout Nexus here.
 * After installation of Broken Steel Scribe Rothchild disappears after giving him a few Cameras.
 * After installation of Broken Steel you are unable to give Scribe Jameson the Brotherhood of Steel holotags.

Follower glitches

 * After Sarah's "So much for celebrating" dialogue if Fawkes is told to enter the code, his dialogues are not heard, and when he enters the room, he just stands at a place until there is the explosion.
 * Star Paladin Cross refuses to follow you when she appears beside your hospital bed in the Citadel after you've completed Take it Back!. After telling her to follow you she stays put, yet her dialogue options change as if she was following you. The only way to get around this bug in the console versions is to fire and re-hire her. That will make her follow you again, but this problem will resurface any time you tell her to wait in the future. For the PC version, you can permanently fix this problem with the GECK. See the Talk page for a step-by-step walkthrough of how to fix this bug by using the GECK.

Level-up glitches

 * When the player reaches level 20, the skill or perk screen may not show up and the player stays at Level 19 while their experience keeps rising past the maximum amount.
 * This has since been fixed in a released patch.
 * As the player levels throughout Level 21-30, their Karma title will not change. Three Dog will still refer to the character with their appropriate title, but the Pip-Boy 3000 will not address the new Karma titles provided in Broken Steel.

Purified water glitches

 * If a player starts a new game with Broken Steel already installed, when listening to GNR, Three Dog will sometimes make reports on the Purifier being retaken from The Enclave by the Brotherhood of Steel and clean water flowing into the Potomac River, despite the fact that the player has not reached that point in the game.
 * When a non-player character drinks FEV infected water (in combat, usually), you'll get the message "Continued consumption of FEV laced water will be fatal" as if you had drank it yourself.
 * Contrary to the bottling of Aqua pura and to reports all across the Capital Wasteland of free Purified water from the river, the Potomac River is still irradiated, even right in front of the Purifier.
 * Aqua pura crates appear in front of Evergreen Mills, even though the Purifier hadn't been activated yet.

Liberty Prime's head

 * After finishing Death from Above, Liberty Prime's head will appear both outside the Satellite relay station and inside Citadel lab.

Exploits
Please see Broken Steel exploits.

PC only

 * After adding Broken Steel, there is a marked increase in the number of times/places where Fawkes is "stuck," especially when walking through places where he is too big to fit and must crouch. Examples of this are in metro tunnels where the floor drops out and creates a path, or some places in Rivet City. This also happens at random points, where Fawkes will be stuck in a cliffside or rock cropping, partially exposed. He will react to being spoken to but not to your movements. You can fast travel next to him or simply move to a different section of the building and he will be by your side again.

Xbox 360 only
as the door will still say "Key required" even after talking to the paladin out front.
 * When trying to enter Rockland car tunnel you can not gain entry
 * Dead non-player characters throughout the game may disappear once Take it Back! has been completed. One such involvement is all of the dead non-player characters in Old Olney and the Old Olney sewers (Old Olney Underground is not affected however). As a result, the Prototype medic power armor can only be obtained before Broken Steel starts.
 * Adams Air Force Base map glitch (see here). Walk outside the map on Xbox 360