Can I challenge a paper already published in a peer reviewed conference/journal?
I think you have to further examine your motivation for wanting to “challenge” these substandard papers.  All of the following are reasons which are suggested in your question.

You feel that contentless or decisively problematic publications bring down the quality of the academic community as a whole.
You feel that the people who are publishing these works get too much credit.
In particular, they are holding themselves up as superior to you.
Specific people – e.g. you – suffer when you try to rely on publications which do not do what they promise.

This is a lot to answer, but I’ll take a stab at it:

This is a disturbing trend in the world of academic publication.  I now get more “journal spam” emails than all other spam put together (well, counting only what makes it into my inbox).  One can no longer assume that an academic publication is reputable, legitimate, or sincere in any way without having prior specific knowledge of the people and institutions involved.  I think this is a terrible problem, but it's well beyond my pay grade.  I do not have a solution in mind.

The best revenge is living well. In line with point 1, there is an increasing segment of the worldwide academic community in which people, in order to maintain their very low-paying academic jobs, simply must meet a certain quota of authorship.  No one cares about the content or quality; in many cases there is no infrastructure there for them to evaluate the content if they did care.  This is very sad.  At an individual level, what seems best to me is just to get out of this part of the academic community.  In many cases this is best accomplished by relocating to a different part of the world where the academic infrastructure exists.  You are not going to get a job at a research university in the United States by having 50 bullshit papers: that's just not the way things work here.  However, if you are a scholar in India, you can get offered a job in the United States (or Europe or Japan or...) on the basis of your work: it just has to actually be very good.

The person who tells you that he’s right and you’re wrong because he has twice as many papers as you is on the one hand an asshole.  On the other hand, he’s splashing around in a pond that you want to get out of: I can assure you that there are many academic environments in which who's right is not decided by counting publications.  You sound like a serious person: get yourself into one of these environments.

This seems to open up another can of worms, but relative to point 1 above: you simply cannot uncritically take publications at face value.  To be honest about it, you can do this to a greater or lesser degree according to the level of trust and esteem you place in the author, the journal, the institution...but doing this at all is a compromise we make only because we are finite beings living in an imperfect world.  Learn to develop a “nose” for what is correct and what is problematic.  Definitely do not accept a work-for-pay situation which is predicated on the assumption that an unvetted academic work does everything that it promises!
In general, I would say that point 4 is a good reason to challenge papers: if you sstumbled by relying on a paper or can imagine another serious, reputable person doing the same, then you owe it to the community to try to get the word out about the defects of the work.  But as above you should also understand that part of being a good academic is knowing what looks good and what looks bad.  There is an ever-expanding sewage sea of worse-than-useless academic papers.  You can't take responsibility for getting rid of all of them.  But you can teach yourself to avoid the unpleasant experience of being submerged in this sewage sea, and you can teach your colleagues – and, as you get older, your mentees – how to do the same.


Good luck.