A while ago, we read a paper published in a quite credible journal (impact factor around 3), which we believed had a few very basic but significant mistakes in the methods and final results.
The journal's guide for authors mentioned the possibility to submit a discussion ("Discussion: A short commentary (1000-3000 words) discussing an article previously published in XXX."). Together with a colleague, we decided to write a discussion manuscript highlighting the problems of the paper in two pages. We did it twice, actually—one time very polite, and a second time more to the point.
Although each time all of the reviewers agreed on the highlighted problems and one reviewer even recommended publication "as is," both times it was ultimately rejected, because the editor focused on a comment of the reviewer like: "was not general enough", or because "it is more a discussion, and not an original research contribution." (But this was actually exactly what was intended, and fully in agreement with the objective for this type of manuscript in the guide for authors.)
It is OK if a manuscript is rejected (I am a PhD student because I like to learn new things), but it should be rejected for the right reasons. The arguments against the article did not seem to consider properly the submission type, "discussion" instead of "original research article." Furthermore we have the feeling that the editor could be embarrassed to publish a discussion highlighting a paper with such errors that could be recognized by frankly any above-average high school student. (although the paper has been cited quite a number of times, apparently without anyone noticing the mistakes).
It is probably not worth the effort, but it became a matter of principle. We contacted a few other people (not our friends) in the field for a quick opinion about the manuscript, and they confirmed our impression that it has probably been rejected out of embarrassment. This seems quite a disgrace, but what can one do about it?
Should we publish the manuscript together with the reviewer comments on our group website? Submit the manuscript to a competing journal? Would it make sense to contact the publisher (Elsevier) to complain about the editor in chief?
I should also mention that the writers of the original article are, according to their group website, co-sponsored by a big company which gains obvious advantages from their erroneous findings. Is there maybe an ombudsman to which we could go to?