Best description I've heard for this is "institutional knowledge". It is not uncommon for a workflow/process to be "well documented", but over the course of time, the people that actually do the process have found small little tweaks that are not part of the original documentation nor do they ever get added to the documentation. Due to this, following the directions will never result in what the current workflow does.

You see this a lot in recipes, and I've heard tales of military being susceptible to this, large manufacturing processes, etc where the tweaks are susceptible to being lost if large cutbacks/layoffs were to affect the people with that tribal knowledge.