In reference to this issue:
jekyll/jekyll#2854

Redcarpet has started to interpret some html/js code as Markdown which it didn't do before. My change was to update Jekyll, which maybe has also updated the dependency to Redcarpet.

Please see this script:
https://gist.github.com/grobmeier/f2222332ffe86dbf485c

Which outputs:

ruby app.rb
<p><script type="text/javascript">
    google<em>ad</em>client = &quot;ca-pub-000000000&quot;;
    google<em>ad</em>slot = &quot;000000000&quot;;
    google<em>ad</em>width = 1;
    google<em>ad</em>height = 1;
</script></p>

I had to remove Redcarpet from my Jekyll installation and use Kramdown which works as expected.