Writing a comment, the consequences 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.
Yes you made the right decision of submitting a comment to the paper. Publicly commenting papers happens much too rarely, for reasons that may be at least partly technical. (Compare publishing your comment to writing here at StackExchange in terms of time and effort.)

As for future consequences, nobody knows. But if your comment is good, journals editors could get the idea of soliciting you for reviewing papers.