Spoiler warning! This section of the article contains spoilers, or hints about the game's storyline or progression.
You might want to skip down to the next heading if you do not want facts about the game's storyline or plot revealed to you.
Sometimes, after the first Shadee fight, you will load your game to find yourself as the Sand Wraith. He's dressed all in black, has glowing eyes and loses health. If this happens, you cannot continue in the game, as a necessary cut scene won't be triggered. You must revert to an earlier save.
Sometimes after restoring from a game saved in a portal room, the prince will only be a floating head and weapons. This is a harmless glitch and doesn’t keep you from progressing.
If you get all life-upgrades as early as possible (meaning before the mask of the wraith), when you enter the hourglass chamber, the cut scene from before you fought the Empress will play again and a boss health bar appears. You can still go through the same hallway you normally would, but it dead-ends. There is a work-around, though. Head right at the end of the hall and you'll glitch through the wall and appear in the throne room. The Empress is there, but you can't fight her. Smash the back of the throne to gain access to the time portal. Go in and save in the portal room before going through the portal. When you go to the present, there will be no room, only black space, and you'll fall to your death. If you select "retry" on the game over screen, it will work correctly the second time, however. After this, the game should continue as normal.
Sometimes, at the end of the game, you will not be able to go through the portal behind the throne room. It is unknown what causes this and there is no work-around. You will need to go back to an earlier save.
In the first Empress battle, the prince sometimes gets stuck in the floor, and then drifts into a wall and dies. Just retry. This isn't a persistent glitch.
Liquid floor 2
In the second Empress fight, if she uses a teleport attack while you are hanging off the edge, she can get stuck in the floor. There is no way to damage her, so you'll have to kill yourself and retry.
Liquid floor 3
When returning to the room in the mechanical tower where you activated it late in the game, the final gear shaft sometimes become impossible to stand on. The prince will fall right through it. The same is true of the floor on the other side of the window. It is possible to wall-run to the window, jump from the window to the artwork chest and jump from the chest to the other ledge and thus get down anyway.
Also when returning to the activation room in the mechanical tower, it is possible to fight the golem without him stepping on the platform. If you beat him, it will raise a level whether he's on it or not, however and can end up blocking your path, though you can still get out via the other route by swinging on the gear shafts.
When returning to Dahaka chase areas, sometimes the screen will turn sepia again and tentacle effects will appear. This is a harmless glitch. Play can continue as normal.
If you return to the sacrificial chamber after completing the Sand Wraith Segment, you cannot leave. You aren't supposed to be able to get back out the way you came and if you attempt to leave the same way you did before, you will find that it is no longer possible to grab the ledge in the present antechamber you used to escape this area the first time. The prince simply hits it, and then falls to his death. There is no workaround. You must restore from a save before you entered this area. If you don't have the life upgrade in this area yet, there is no way to obtain it.
At the end of the sand wraith segment, if you go back into the library rather than leaving the mechanical tower, scripting is broken and when you do attempt to leave, the platforms will be in the wrong position and no cut scene plays. If you restore a save at this point, you are back to being the regular prince instead of the wraith. There is no known work-around.