When you have a problem in an agile environment, you first try to hack the world around it to make it visible. Make verbal communication and silent promises appear on the walls, use information radiators to show overuse of key resources, make dependencies impossible to miss etc. Oh how much do I love my colorful Kanban boards! 
More often than not, what you will discover is not the real cause of the problem but a mere symptom of something bigger. More often than not, you should iterate and you work with this new symptoms to try and make one more cause visible. Repeat until you reach a cause that is big enough that you can make a whole bunch of problems disapear at once.
In praxis, it is oh not that easy. I was never (and will never be) able to identify the root cause of a problem at first glance. What I work with is guts feelings. Whenever I smell something fishy, I attempt to visualize it. Like the observer effect, the mere action of trying often reveals new information. In a way it is like finding a painful spot (symptom), put your finger on it and pushing more or less hard against it.
Make the pain visible is not often easy. But preventing easy remedies is often harder. Remember, you want to find the real cause of the issue, not solve make the first symptom disappear. And we are problem solving machines after all. More often than not, you need to swallow the pain and keep pushing. In a way, agility is some kind of pain driven development. Whenever it becomes painful, we embrace it for the greater good . You know the drill: "if it hurts, do it more often".
So afterall, are we just a buch of masochists?
PS: This message has been brought to you by an agile coach who was elbow deep, arched on a painful spot in the organisation, really sure we were making good progress in finding the root cause, took a day off and came back to find an organisation high on "pain killers" having made a few symptoms disapear without caring for the cause itself... #meh :'(
 Do you know the Toolbox for the Agile Coach book by Jimmy Janlén? You can buy it on Leanpub and it's well worth its price. Here's a link to the free sample PDF.
 Whoever has experienced the joy of an hyperproductive team / project / organisation will tell you, we will go through all that pain three times over just to be able to experience that high again!
Image Source: Pain by ***nico7523*** (CC BY-NC-ND 2.0)