Ok, so is there some limit to how much you can enter a pet into battles? because I used my main pet alot the other day and now she doesnt even show up on the list to fight....

She's probably stuck in battle, or maybe she has 0 hp? Check the Statistics page

Didnt think to check that.... thanks

If you're talking about E_xtacy, it looks like she needs to be healed. Pets can't battle if their health is zero.