The human body is incredibly complex, and most studies look at incredibly specific effects. "increases lifespan by x years" takes decades to measure, but "increases blood cholesterol by x" can be measured much faster. So in the interest of getting papers published in reasonable timeframes most studies take the latter approach.

Then comes media, sees "X causes blood cholesterol to rise, cholesterol is bad, so X is bad" which is a deeply flawed conclusion. Most things aren't universally bad (high blood pressure is bad, but if you raise your blood pressure through exercise that actually lowers blood pressure in the long run), and many negative effects are offset by positive effects not looked at in the study. I wouldn't read too much into anything that isn't a metastudy and took less than a decade to test.

I think the current consensus about red whine is somewhere along the lines of: red whine is good for you, the more you drink the more that effect is offset by negative effects of alcohol, but in the amounts that were always recommended (about 1 glass a day) it's not a huge factor.

But of course those are the harmless examples, there's also interference from industry groups interacting with the current publishing environment (see the whole "fat is bad for you" that we had going for decades for no good reason). So there is a lot of room of improvement.