Due to some fairly serious diet-related personal health issues (obesity and several related co-morbidities), 5 years ago I started closely following nutrition science. In this time, the clearest thing I've learned is that the vast majority of "Nutrition Science" is poor science - to the extent of hardly being science at all.
* If the data is based on diary data, it's noisy to the extent of being nearly useless and no causation can be implied.
* Doing rigorous controlled studies on humans is very difficult and astronomically expensive. Even then, it's incredibly easy for significant confounds and errors to slip in.
* With nutrition studies in general, animal models are usually weak proxies for humans. A large number of significant nutrition results in animals fail to replicate in humans.
* Humans metabolic responses to nutrition are highly variable and contingent on everything from genetic make-up and ethnicity to behavior and environment, etc. So, even in the rare cases statistical causation is demonstrated, it probably still depends on other variables.
* There is a high degree of bias in nutrition science. This includes many funding sources having vested interests from commercial (food lobbies (meat, wheat, milk, etc)) and many researchers having ideological biases (anti-meat vegetarians, anti-meat climate concerns, anti-meat animal welfare, etc)
* Accepting any result as significant requires skeptically examining the methods, statistics and history of the authors and funders.