According to this study, when developers are show then definitions of <section> and <article> without the element names, they often confuse which goes with which: <http://adactio.com/journal/1654/>

I suspect this may just be due to awkward wording. The section definition says:
"The section element represents a generic document or application section."

If you're skimming and the element name is removed, this can easily look like: "The ____ element represents a document".

I think wording similar to this may be more clear:
"The section element represents a generic section of a document or application."

Maybe even drop the word "generic" from the first sentence. That way, the sentence more strongly conveys the impression that the section element is a section.

The article element, in turn, says:
"The article element represents a component of a page that consists of a self-contained composition in a document, page, application, or site and that is intended to be independently distributable or reusable, e.g. in syndication."

Again, reading quick, this might look like: "The _____ element represents a component of a page".

Here's a suggestion for possible better wording:
"The article element represents a self-contained composition in a document, page, application, or site that is intended to be independently distributable or reusable, e.g. in syndication."

That puts the "self-contained concept" concept front and center, instead of "component of a page", which is secondary. An article could be substantially all of the content of a page, it doesn't have to be just part.

I think wording changes along these lines may reduce confusion.