Sound and effective policies, informed by reliable science, are needed to ensure sustainable well-being of oceans and marine resources. Scientific publications often influence evolving policies and inform the public, but sometimes contain errors. The prevalence of papers conveying unjustified messages and with potential to influence public perceptions and policies is concerning. This paper focuses on marine examples that have led to exaggeration of negative impacts on ecosystems, particularly from fisheries, but the criticisms and recommendations also apply more generally. Examples are given of papers on high profile topics that used flawed assumptions or methods, leading to some misleading findings. All examples were eventually followed by published rebuttals. Such papers, often accompanied by media campaigns, can lead to inappropriate policy choices, and other negative outcomes. Science is eventually self-correcting but often too slowly to prevent flawed perceptions and policies. Problems should be corrected before publication. A common weakness in the publication process is inadequate peer-review. Shortcomings at the level of editor can also contribute to the failures. Pressure on scientists to publish, leading to increasing numbers of papers, puts reviewers under more pressure and makes it harder for editors to find suitable ones. Recommendations to avoid the impact of flawed science on policies are made within the framework of a three-legged stool consisting of: (1) scientists who strive for objectivity and accuracy; (2) journals with editors and referees better equipped to guard against unreliable scientific publications; and (3) transparent and inclusive scientific processes to formulate advice on policies and their implementation.