Rejection is the norm in academic publishing. Even researchers at the top of their field have experienced rejection. What are the possible reasons of for manuscript rejection in journals?
There can be many reasons for rejection of an article. In case, the work is not original and merely repeats the work already published or unsuitable for the journal by way of its mandate, the article will not be accepted. Sometimes, the article may be too long or the article is written badly and is difficult to read. Presently, editors also check for plagiarism, and if it is above a limit, your article will be rejected. Similarly, if the journal editors have doubts about the validity of results, the article will be rejected.
If the authors feel that the referee’s or editor's criticisms are unfair and invalid or that the referee has misunderstood your interpretations, you may write to the editor detailing your points. The author can explain why s/he disagrees with the referees, and suggest some modifications to make the paper more meaningful. If the points raised by the authors are reasonable, most editors send the paper to a third referee!