Nutritional epidemiology is a very complex area; eggs are a case in point. Evidence has been emerging that eggs are better for you than we had previously thought.
(h/t: Obesity panacea)
My SO (who does nutrition) has pointed out that we often look at just one part of a food and forget the other aspects. The result of simplistic recommendations may result in unbalanced diets -- a focus on fruits and vegetables can overlook important elements like adequate dairy intake. It's just hard to reduce to dietary recommendations to sound-bytes. Add in individual differences and the complexity of the problem increases (a lot).
Nutrition is a complex system with dozens of exposures (both macro- and micro-nutrients) that has significant issues with data collection. Food frequency surveys have known limitations and more sophisticated measures have their own limitations. Experiments are also difficult to design given the complexity of nutritional requirements across the lifespan.
It's not easy stuff!