[1] The journal states that their aim is to assess solely the scientific validity of a submitted paper, rather than its perceived importance, significance, or impact.

[8] The Guide to Referees states that to be published, "a paper must be scientifically valid and technically sound in methodology and analysis", and reviewers have to ensure manuscripts "are not assessed based on their perceived importance, significance or impact",[9] but this procedure has been questioned.

[10] Allegedly duplicated and manipulated images in a 2016 paper that were not detected during peer review led to criticism from the scientific community.

The paper alarmed public health advocates in Japan and worldwide because of the potential side effects of the HPV vaccine on humans.

[22] Scientific Reports retracted a 2019 paper in January 2021 which claimed that "both Creationism and Big Bang theory are wrong, and that black holes are the engines driving the universe".

[25] A paper published in September 2021 implied that the Biblical story of the destruction of Sodom and Gomorrah might have been a retelling of an exploding asteroid around the year 1,650 BCE.

"[27] In 2015, editor Mark Maslin resigned because the journal introduced a trial of a fast-track peer-review service for biology manuscripts in exchange for an additional fee.