I don’t know if this might be a bug.
This is the code I have before indentation (html5 doctype):
<ul>
<li><a href="../docs/introduction.html">Introduction</a>
<li><a href="../docs/options.html">Options</a>
<li><a href="../docs/methods.html">Methods</a>
</ul>
And after indentation I get:
<ul>
<li><a href="../docs/introduction.html">Introduction</a>
<li><a href="../docs/options.html">Options</a>
<li><a href="../docs/methods.html">Methods</a>
</ul>
It seems ST2 has problems with open tags in html5 syntax