If a faerie has blessed your Neopet with a new ability you will have to activate it before it will be able to be used by that pet in the Battledome.
You can check on all of your pet's abilities and activate them from the Quick Reference page here http://www.neopets.com/quickref.phtml.
Click on the arrow next to the pet with the abilities you want to view and select "View Abilities."
Alternately you can visit the abilities of your active pet going here.