The JWT expiration setting within the client application configuration applies to an ID token issued to the client application itself. In general, if you’re calling an API you will be using an access token like you said.
The access token may also indeed use the JWT format so I agree the above naming can be confusing. For an access token issued for an API you created in the dashboard the lifetime depends on the settings configured in the API configuration itself.
The first thing to check would be to confirm that you’re indeed sending an access token and then check the API settings to see if any of the expiration settings would explain what you’re observing.