Over the past few days Ive been attempting to trap pets I am interested in.
It was all going fine, until I tried to catch one, it worked, and then the pet was nowhere to be found in my stable.
This has happened to me twice and both times I am SURE I caught it...what is going on?

Did it actually say in the battle log that the pet had been caught and added to your stables? If not it may have been defeated or even have ran away

Link: https://www.sylestia.com/forums/?thread=7244&page=1#8 Author: Talyn Time Posted: 10/30/2013 at 5:56 PM When using a trap on a pet there are three outcomes that will give you a victory condition: 1: You successfully captured the pet (There will be a link to the pet's page in the battle log) 2: The pet got scared and fled. (A lot of people will get this result and think that they have caught the pet when they haven't because of misreading or assumptions. You will not gain any EXP from this.) 3: The trap failed and the pet took enough damage to loose it's remaining health and was defeated. (This can happen if you chose to attack the pet instead of guarding or if they had a status effect that causes them to loose health. You will gain EXP from this.) These results will only be visible in the battle log at the end of a battle and before you close the battle screen. If you close out without seeing the result, the only thing you can do is check your stable. If the pet is not there then you can assume that the pet fled and thus was not captured.

If this helps.

it does, thanks :)