At times it may be difficult to recognize cause. If a system responds to infection, (let's say), with quick countermeasures, it may be difficult for observer analysts to recognize the infection for what it is: countermeasures may be labeled simply as syndrome, and cause is masked. Cases where underlying mechanisms have emerged only slowly include present understanding of intestinal flora, asthma, perhaps also how pathogenic exposure in poor childhood hygiene can lead to longer term benefits. We can hope ultimately that scientific methodologies will clarify what is happening. Are there many remaining cases where our imperfect knowledge of physiological, social or other interactive mechanisms clouds understanding?
There are phenomenon where observer interference is difficult to exclude. Perhaps our excitement at getting near may put something further away…