<p>Retraction of scientific papers may occur when the peer-review or publication process is compromised, even in cases where authors have no responsibility for the identified shortcomings. Using a recent case in which a peer-reviewed open-access mega-journal retracted a series of articles due to compromised peer review, also one from our group, this work examines the implications of limited editorial transparency in the retraction process. While failures in peer review can undermine the integrity of the scientific literature, inadequate communication by journal editors may have substantial negative effect on affected authors, particularly early-career researchers, including disorientation, humiliation, and a sense of perceived injustice. This analysis highlights the factors contributing to these outcomes such as the sense of loss associated with the substantial time and effort devoted to the research, as well as the practical impossibility of submitting the retracted article to alternative journals. Transparency represents a frontline defence against research misconduct but the call for increased transparency cannot be one-sided. Transparency needs to be a useful tool for the entire system, for those who report data and for those who publish data.</p>