Usually, with the case of catapults ... artillery, the problem is with an enemy unit being or coming adjacent, which cancels orders (as set in your preferences).
As with any unit set on automatic, it is often difficult to determine WHEN the actions will be executed. Often, it is later than I want ("I want to attack NOW, like execute the bombardment already -- please!"). Also, I almost have to Sentry my assault units because I keep being prompted to move them while waiting for the auto-bombards.
So, the bottom line is: Had you waited until then end of your turn before you "decided" they weren't going to do it??