Not being FDA approved, is not the same as being contraindicated for use. Many medicines are not approved for use in pediatrics, but they are used all the time anyway. Unless a company wants to market it for pediatric use, there is little reason to get it FDA approved for pediatric use, because pediatricians can use it anyway. Seriously, look up some of the drugs that you know are used in little children all the time (like antibiotics), and see what ages they are approved for. So no, just because a medicine is not approved for pediatric use, in itself, is no reason to call the doctor or to not fill a prescription.
Now, with your concern specifically, of aripiprazole, I would want to know the history of what else the pt has been on, and what exactly is being treated. I would question aripiprazole if it's the first drug being tried in a 5 year or younger person, especially if not being prescribed by a psychiatrist, and double that if being prescribed by a non-MD/DO. I think it very well may be appropriate to call the prescriber about this prescription, but the fact that it's not FDA approved for <6 is not the reason why.