Some of those are pretty easy to separate -
Alchohol isn't really good for you - statistically you will probably get away with reasonably low intake but the observational studies showing a benefit were most likely confounding variables - like studies where the 'non-drinkers' category contained those who had been alcoholics and were forced to stop drinking, or demographic distortions where moderate drinkers had much healthier lifestyles in other areas (exercise, access to healthcare, etc.) than heavy drinkers.
Coffee seems to be good for you, as long as it's only up to a few (3-4) a day, and as long as it's not affecting your sleep. But I have read the fines in methods like Turkish coffees could be somewhat harmful, whereas espresso is fine and paper filtered better. Sweetening it with sugar isn't great for you of course.
One that gets me is dairy and milk, I get the ethical concerns, and one can make an argument that it's not super 'natural' to take another species milk and to drink it after infancy, but that doesn't mean it's unhealthy (almost all medicines are 'unnatural' too, while some poisons are fully natural!). There's some evidence of milk/dairy being protective against bowel cancer for instance, and inconclusive evidence of harms so I do wince a bit at the plant-based milk alternatives (which are highly- or ultra-processed, if you do care about that kind of thing!) being so trendy.