3.6 breaking links

I’ve had a few clients complaining that after they’ve upgraded to 3.6, then they tried to add links to shortcodes or other HTML the links never work on the frontend, although this is what I get from the source:

<p><br><a href="plan-your-ecotour"><span class="button extra-large">PLAN YOUR ECOTOUR</span></a></p>

While inspecting i get this from the exact same line:

<p><a href="#"><br></a><span class="button extra-large">PLAN YOUR ECOTOUR</span></p>