Sorry for the delay. It looks like you might be using Embedded App SDK methods that are incompatible with App Bridge. Are you using any of these?
'ShopifyApp.Modal.input',
'ShopifyApp.Analytics.fetch',
'ShopifyApp.Nav.initialize',
'ShopifyApp.Nav.select',
'ShopifyApp.Sidebar.setSection'
You have a feature enabled on your app which would enable the use of the Analytics API for example, which at this time cannot be used in tandem with App Bridge.