What should be included as part of a comment paper? I intend to submit a comment paper. In the base paper the "basic assumption" made for justifying the result is wrong. I intend to cite some reference books which support my argument about incorrectness of basic assumption. 

My question is whether I should just list the facts with proper citation OR also justify that by some experimentation? I have an alternative justification which could explain the results. Should I perform experiments and prove correctness of justification that I propose?
should [I] just list the facts with proper citation OR also justify that by some experimentation? 


You should give some intuition behind facts. You needn't justify established facts with experimentation, but doing so may provide useful knowledge. If facts aren't established/accepted, then experimentation should be provided. 


  I have an alternative justification which could explain the results. Should I perform experiments and prove correctness of justification that I propose? 


For a comment paper, you surely need only provide facts that show the "basic assumption" made for justifying the result is wrong. 

For a research paper, you could provide an alternative justification which could explain the results, along with experiments that prove correctness of justification that [you] propose.