The background: I work in a quite narrow field in physics. Recently I submitted a comment on a published paper. Before doing this I discussed my remarks with the authors directly and they gave me some interesting suggestions and comments. In the end they suggested to publish as a rapid communications instead of a comment. However, I was more convinced that it was something it should be corrected and replied that I find a comment more suitable (assuring them this is of course nothing personal). However, a bit after this my doctoral advisor said: "feel free to submit but please remove my name (you can acknowledge me for useful discussions and proofreading)". I have a feeling this is related to the fact that he has some limited contact with the authors.
My questions: Did I make the right decision of submitting? Will there be any consequences in the future (regarding Refereeing). I really have nothing personal against they authors (which are in fact very competent authors who have published many interesting works).
I would like your opinions on this situation.