This is relevant to the other thread too, but I thought I'll just post my comment here. It is a combined answer to the questions asked in both threads.
The other question, which reads "Are specific questions about Theorem X in paper Y fine?" actually covers two types of questions from posters.
Type 1: Questions like "How does one reach eq 3.14 from eq 3.15 in paper X, page Y? I tried the following ... but it didn't work."
I think most people would agree that these questions are appropriate for this site. The other type of question is the following:
Type 2: "How does the proof of Theorem 3 in [citation] handle the case of disconnected graphs? I don't see how it works for that case."
This question might be pointing out a genuine error in a paper. But then again it might just be something the poster did not understand. What I want to say is that it is often hard to tell whether there is a mistake/confusion/non-understanding on your part, or an error in the paper. These correspond to type 1 and 2 questions respectively. If the poster is not able to distinguish between the two types of questions, and if we make it a policy to only allow Type 1 questions and not Type 2, this will be hard for posters.
Would a solution like the following work?
We allow both type of questions. Questions of type 1 are handled as they usually are by the community. If we realize that it is a question of type 2 (i.e., there are answers which indicate that there is a genuine mistake in the paper), then a moderator emails the author of the paper and informs him of the thread, and offers to have the thread deleted.
Now the author may choose to have the thread deleted, or reply on the thread explaining how the poster has misunderstood and it is not an error, or reply thanking the poster for finding the error, or do nothing, etc. (I am assuming that moderators can delete threads.)