I also substitute teach in elementary which is k-5. MANY kids have phones and for good reasons. My 16 yr old had her first phone by 4th grade.
School policy is not to have them out at school or they get taken up, this also means at lockers.
I personally don't have an issue with phones at school as long as they are not used in class. I do know our elementary school is strict with the phone policy. Just last week when I was there, a phone was taken up because some kids were videoing each other and the principal had a fit about it due to privacy issues, etc. I do know if anything has any type of gun, drug, etc that ISS happens.
Maybe the school is using your son as an example... sometimes that happens. I just look the other way when I see kids getting ready to go home and pull a phone out to text mom or something. Like you said, they are at the locker.
If I saw this app or game being played at the locker, I might take the phone up if it was causing a lot of negative attention or simply talk about the app being inappropriate and have your son place the phone in his backpack for the day. It would depend on the "attitude" I got from your son.
In High school, phones are no longer banned unless they are being used in class. My 11th grader texts me all day with updates, etc. Most of the teachers are open about it as well unless of course testing is in progress, etc.
I probably would not punish my daughter when she got home. I would just remind her that some things are taken WAY more seriously and to avoid the situation by taking herself out of the situation which means, keep the phone in the backpack. You know the school policy now and how they reacted so you know how much leadway you have.
A bit tough punishment, yes.