If the agency registered your domain in its name, it holds the keys
If the agency opened your domain, your app store account and your code repository in its own name, you paid for the work and someone else holds the keys.
It happens in the first week, usually for good reasons. The agency wants to move fast, nobody has the company card handy, and someone sets up the accounts so work can start. Nobody comes back to move them.
Nothing goes wrong while the relationship is good. It goes wrong the day you want a second developer, a second opinion on their work, or out of the contract. Then the question stops being what the app is worth and becomes what the agency will charge to hand over things you assumed you owned.
The contract may say you own the work. Ownership on paper and control in practice are separate problems, and only control keeps the business running on a Friday night when bookings stop.
This week, make a list with two columns: every account the project touches, and whose name and email it sits under. Domain, hosting, app store listings, the code repository, the email sending service, analytics.
Anything in the agency's name moves into the company's name now, while everyone is still friendly. Some transfers take a few days of paperwork. Later they can take a lawyer.