Um, the "Bad Stuff" section doesn't say anything about the 'Advanced' alert cards.
...but neither does my rule book say to remove them from the deck. (I have version 1.1.)
Actually I only noticed halfway through the game that some of the cards said "Advanced" on the back. Am I supposed to do anything special with these cards?
Advanced alerts should be removed from the game until you are comfortable with the game. Once you are ready to use them you will replace some existing alerts with the advanced ones. Simply pull out a yellow alert and replace it with an advanced yellow alert.