Thanks so much for getting in touch!
You're absolutely right that there are a number of potential reasons for this charge, one of which may be an app, which you'll see included in our guide Understanding your bill. That said, based on what you've shared, I imagine your store has been automatically upgraded to our Pause and build plan ($9 USD/month), which will occur after 3 months on our Full pause plan. Does this sound accurate based on when you originally paused your store?
If your store is now on our Pause and build plan, you should be able to log in here, then visit Settings > Billing > Recent bills to confirm the source of the charge(s) for sure. Let me know how that goes!