Publishing articles that are critical of previously published work is notoriously difficult but the secrecy of peer review makes it hard to explain the kind of biases and tricks that one faces in this enterprise. Opening peer review, i.e. sharing reports and responses, would certainly help. Here is an interesting exemple related to an article (nicely discussed by Philip Moriarty in a previous post) which is not even critical of prior literature but touches on the stripy nanoparticles controversy. That was too much for Reviewer #1 (hyperlinks added by me; they point to relevant blog posts here or at PubPeer):
Reviewer #1 (Remarks to the Author):
This paper describes the scanning tunnelling microscopy imaging (STM) of a silver cluster (Ag374). To the best of my knowledge there is no report of such things to date. As such I think this paper should be published but in a specialised journal or a broad journal with reporting functions as Scientific Reports.
The significance of this paper as such is minimal. The STM does not add anything to what X-ray crystallography has shown so far also on the same cluster. In fact it requires strong support from calculation.
The STM itself has been widely published on nanoparticles by the group of Stellacci. The authors do reference a controversy there but do not comment on it an neither add to it.
The approach used is almost identical to the one described by such group in Ong et al ACS Nano (non cited), and the results achieved are similar to the ones described in the same paper and in Moglianetti et al. (not cited). Their minimal difference is that they achieved these results in liquid nitrogen and helium temperature, but low temperature results were described in Biscarini et al. (not cited).
Given the scant discussion in the paper (lacks any point) and the two major objections report, I suggest rejection.
The other, more supportive reports, and the response from the authors, can be downloaded from Nature Communications.