Mothership Dominates LESS module
Mothership does NOT make sweet love to the LESS module. They both do their magic with the $css and there can only be one - actually mothership brutally overwrites whatever the LESS module wants to do.
This is because the LESS module wants to compile the .less files into .css files as the $css is built and Mothership tries to clean out all the crap *ahem*.
A workaround is to do the compiling locally with CodeKit, or man up and compile it with the terminal and Ruby…or join the grown-ups and begin to use Sass & Compass - which are also compiled locally before added to you CSS.
Ajax & Comments
Disable the comments from poor theme developer. These comments are known to cause problems with Ajax.
Bug Reporting
Just to make it clear the Mothership is NEVER to blame! - It's always Drupal's fault (this hasn't been confirmed 101% yet by @drupaltruth though).
If it should happen that there is actually a bug somewhere, please use the Mothership issue queue for this. http://drupal.org/project/issues/mothership
If you need support, check the forum. If you want help with your theme and have gold in your pocket, contact the captain.