I know this topic is a bit old, but I just had the same issue and a Google search points here.
If your packet is working correctly, and its just the warning in the log, you've likely made the same mistake as me.
Inside the "messageConsumer" you provided when registering your packet, you need to set the packet handled flag to true. "context.get().setPacketHandled(true);"
If it isn't set to true, NetworkHooks.onCustomPayload will return false, and ClientPlayNetHandler.handleCustomPayload will post the warning