In the couple of instances I experienced this, the problem is that the system is like the proverbial elephant that a bunch of blind people are familiar with through touching the parts they are next to; but the complexity is in the relationships in-between.
There needs to be a person who will take charge and learn/document the whole system, except people who work on it are overloaded and too exhausted to take this on. And management doesn't necessarily have the insight or incentive to make this happen. It's an interesting phenomenon.