I set up a Fireknight team with Panthera set to not use her "Vanish to Shadows" skill.  In single battle this works fine, but not in multibattle, she keeps using it.  On looking closely, you can see this is because multibattle drops/ignores the team setting.  I have tested/repeated this in both Fireknight and Dragon.

To repeat/verify, run a regular single battle with "Team Setup" enabled/used (the Team Setup button goes from gold to blue to indicate it is set), preferably with one of the champs set to not use one of their skills.   During the battle you can observe them properly not using that skill, and on completion of the battle, if you hit the "edit team" button the "Team Seteup" button will still be blue (enabled).  

If you then try a multibattle, whether set to just one or more, the AI will not honor the selected AI controls and upon multibattle completion if you hit the "edit team" button the "Team Setup" button will be gold (not selected/enabled).