|In some cases, employee shortcuts are actually a better way to do a particular job, while in other cases these shortcuts can short circuit an entire operation.|
The real question focuses on your department manager. If he or she is aware of the shortcuts and feels that they are a better way to handle various operations, then they should be documented and included in the orientation.
However, if your manager is aware of the shortcuts and believes they are compromising quality, then one has to question why he or she is allowing them to be used. It is possible that there is a performance bonus involved here, and your manager has decided to look the other way and focus only on output.
And finally, if your manager is unaware of these shortcuts altogether, one has to wonder how this individual is spending his time.
Since it is difficult for you to do your job under these circumstances, you should meet with your manager to discuss what is going on here. Your manager's response is going to tell you a great deal about what it means to work in this company, especially if his or her reaction to the shortcuts is to cut you short.