Problems I have with research papers that I’ve seen is despite statistically significant results saying otherwise, the authors still purport what they are paid to do by the manufacturers instead of what’s clear and in the data.

This happens often but I just find it more relevant if people argued on the technical details of the research than doubting the conclusion. Sure, it's easy to claim that an agenda backing up the study, I get that, but when motive is the only thing being talked about rather than arguing about the sampling method, statistical tools used, and references I just lose interest on the whole argument about motive. Argue with the technical details not argue with motives that can't be tangible to prove. If BigPharma funds the damn research and wants to make money from it, that's understandable, but when they start publishing questionable results like incongruent data that can be disputed, that's when those claims have some weight.

Makes it very difficult to trust anything besides our own judgement and experience.

Has to do with people having initiative to inform themselves and exercise critical thinking to which it's a self training practiced for years and not just something that one does during their internet browsing. I don't question conclusions, I question how someone arrives to those conclusions when I don't know the subject. Most would just focus on accepting the conclusions. It's difficult to argue soundly with something they don't have full grasp on and accusations like the other party doesn't know what they're talking about is easier than actually sifting the details that makes it rationally so.