How do I figure out what is really wrong in an organization?

Diagnosing what is truly wrong is harder than fixing what looks wrong, and most people never learn the difference. The fact that you feel it eluding you means you already sense there is a deeper layer. That instinct is the beginning of the skill, not the absence of it. Dysfunction rarely lives where the complaints point. People tell you about the symptom, the missed deadline, the tension in a meeting. The real cause is usually quieter: how decisions get made, who is afraid to speak, what no one will say out loud. Look less at what people do and more at what the system rewards and punishes. Next time you are asked to fix something, resist naming the problem for a while. Just watch and ask simple questions. Who has power here, and who feels they have none. The answers you gather slowly will tell you more than any quick diagnosis. Patience is your real tool.