1.) The prospective data collection methods used in a lot of studies are deeply flawed and worse aren't documented.
2.) The retrospective data used in many studies is poorly validated and the quality is rarely a concern for most universities.
3.) The people who publish these papers are very intelligent, most far more intelligent than I am, but you'd be surprised how many of them don't have a very good handle on basic statistics. Not because they aren't smart enough to learn but mostly because they have no interest in it.
4.) There is a lot of pressure put on researchers to publish papers even if they aren't ready and as a result mistakes are made, there really needs to be less of an emphasis on the quantity of papers that are published and more emphasis on quality.
For anyone who might be interested in such things, if you ever find yourself locked in a dungeon with nothing but a computer loaded with every journal article ever published you can find articles involving similar cohorts from the exact same universities that have different results.