HTML5 and Full HTML Filter
I just came across the same issue, and although this is a rather old question I thought I'd give my solution in case any others find their way here.

Text formats have the option to correct 'faulty' HTML, although it's not the best choice if you'd still like to make sure that actual faulty HTML is corrected, you can turn this off by navigating to:

HOME &gt; ADMINISTRATION &gt; CONFIGURATION CONTENT AUTHORING &gt; TEXT FORMATS &gt; %your format%


Deselect 'Correct faulty and chopped off HTML' and Drupal will stop mangling section, article, figure, and other useful HTML5 tags.