And this opened up a whole lot of questions for me since I am studying to go into research, and I wanted to know the opinion of those of us here who are/were scientists and if there really some degree of problem scientific misconduct in the current system of publishing
Is it perfect? Hell no. Is it better than no peer review at all? Hell yes.
Science is not immune to the human element. We all hold the method and data as ideals, but at the same time we are all people with emotions and personal pride. Yes, there is a politics of science. It can even devolve into child-like playground insults. I've seen it happen. Anecdotally, I watched a grad student melt into a puddle of tears right on stage. She was giving a oral presentation at a big conference after which there is always an open floor Q&A. A prominent scientist stepped up and just started bullying her because her findings contradicted his own. This type of stuff happens, for better or worse.
With that in mind, conferences are the way to go to expose what you consider bad science. If someone publishes a paper that is wrong and concludes that your life's work is bollocks then present their work at a conference and show that it is wrong using your own findings. I have seen this done several times (including the sob story above). The reason that a conference is a good place for this type of exposure is that a lot of the big hitters in your field will probably be there if you choose the right conference. These are the same people that will probably be reviewing your future papers, and maybe even your grants. These are also the same people that you are speaking to in your papers. No one else in the world probably gives two cents about your research, but those scientists do.
Yes, there is chest thumping. Yes, there is posturing and preening. However, at the end of the day the data does win the day.