It's pretty much a trope that coffee has been bad for us one week and then good for us again the next week, ad infinitum.
It would be very amusing to see the world through your eyes.
How exactly do you think science works? Do you think that someone asks a question, and then scientists all get together in a single meeting to answer that question, and then they post the answer and claim it is the full and unquestionable truth?
No, that would be ridiculous. Instead, science is performed by millions of individual scientists, who each seek to understand some particular aspect of reality just a little bit better. They perform discovery, form a hypothesis, test the hypothesis, and then publish their results for the world to review.
There is no illuminati-style organization that coordinates all of the scientists, and their findings, together. Thus, one thousand different studies about various effects of coffee upon human health might be performed, and they might all study slightly different aspects of the topic, or test things in different ways. This in no way implies that the scientific method is flawed, or that "scientists" are just a bunch of goofy mind-changers who can never quite figure out which way is up when it comes to figuring out what science actually means.
This is to be expected for something as complex as science, unless you have an extraordinarily simple mind.