If any of the things contained within the pages are contradicted, then throw the manual away. Any exception destroys the policy and procedures. You cannot make an exception for one without making exceptions for everyone. The greatest lost of respect for leadership occurs at this point. When you can't count on the leader's word to be truth, there is no reason to listen or believe anything they say.
Exceptions are the front door to confusion.
Most conversations based on out of control behavior are never completed. Slow down, organize through questions. Don't lose your cool. This is the most important part of creating control. Make the conversation about what needs to happen, rather than what has happened.