I am not a biologist but a physicist. I am used to quite high confidence in the data I have obtained in my laboratory experiments. But from reading some biology papers on vaccines and comparisons with adverse health outcomes I note a whole lot of controversy.
At first that controversy might seem to be about population sizes in the studies, or how the demographics were selected, or how the controls were handled. But from my reading it seems that it is more the conclusions that the authors come to that are the hot button topics.
As a result I have read of several high profile retractions by leading journals. That is after the papers passed peer-review and were published did the problems arise. People objected and, in some cases, a total debacle ensued.