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Salemicus comments on Open Thread, May 25 - May 31, 2015 - Less Wrong Discussion
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What else does it reject?
I think it's important to look at this on a per-discipline basis. Some disciplines have much higher standards of clarity, precision, and repeatability than others. That article you linked looks at statistical studies with a special focus on medical research, but then seems to make the critical error of generalizing this to all scientific research. Do the findings apply to physics? Math? Computer science?
I see papers get rejected all the time for methodological disagreements and failure to cite papers the referee thinks important. More broadly, ideas that are perfectly plausible but contrary to current thinking in a field have a much higher threshold to publication than ideas consonant with current thinking.
But more generally, peer review is normally explicitly aimed at rejecting work judged to be non-novel or non-substantial. That boring replication attempts can't get published should therefore be seen as a feature not a bug. The ability of academics to publish novel, counter-intuitive and false results should therefore also be seen as a feature not a bug.
Oh, I'm sure some disciplines are worse than others. But as you seem to be tacitly conceding, "the vast majority of scientific output never undergoes real review," and that's true in all disciplines.