I have presented in conferences A and B. The work presented in A is published in the conference proceedings (in case it is relevant, it is indexed by IEEE), and the work presented in B is published in a special issue dedicated to conference B. My CV has sections for conferences and articles. Is it the norm to include both publications in the article section and then rewrite them again in the conferences section (in each case, the talk and the paper have the same title)? If not, how should I do it?
Put your articles in articles section, and presentations in presentations section
For a publication that comes out of a conference talk, it is legitimate to list it in the appropriate part of your articles section, and also list the conference talk in your conference presentations section. So as not to conflate the two, make sure that the latter section is clearly about conference presentations rather than conference publications and reference the presentations by conference title, location, date, etc. So long as you are clear on the distinction between published articles and presentations relating to those articles, there should not be any confusion.
You can list both if you do so with some care.
For two things that are essentially the same, you can list one, followed by "Also published as..." giving the second reference.
If one extends the other you can list the more complete one, followed by "Preliminary version published as...".
There are other variations, of course, but if you link them, giving any distinctions, you should be fine.
Only treating them in a CV as independent when they are not would be an ethical issue.