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You're going to have to be specific; which doors in particular are you referring to? I'm pretty sure that there's a few rooms that can't be opened until you've killed all the enemies in it, specifically the rooms where butler and maid vampires show up. If you're trying to run to the door, I'm guessing that'd be why you can't open it.
I suppose that's it. I'm in the Main Castle area (they play the Main Theme music; an extension of the File Selection track), and the door I'm having the most trouble with is a room where those lizards keep coming out of iron doors that you can't enter.
One of the other rooms does have maids and butlers (that scream is priceless, man.) Maybe the game is having trouble with the lizard room because they keep spawning, and it gets confused.