The research methods are the principles for launching a paper. Collection the raw data , filtering the data, analysis of the results and finally the conclusions obtained from the research. All the above should be achieved correctly and precisely.
I would say this question can't be generalized per se. I would talk from the social science perspective only since I belong to that discipline. There are institutions and researchers who develop methodology very meticulously. However, in majority of the cases in social science research methodology isn't formed properly. Hope I could be of value.