Application with identifier was not found in the directory Bot Framework

aymiee - As mentioned here, the cause of this kind of issues might be "the Issuer attribute sent from the application to Azure AD in the SAML request doesn’t match the Identifier value that's configured for the application in Azure AD." 
Steps to follow:

1. Please double check the configuration? This mostly happen when we make mistake while configuring it. Please follow this doc to understand more - https://docs.microsoft.com/en-us/microsoftteams/platform/bots/how-to/authentication/add-authentication?tabs=dotnet%2Cdotnet-sample#azure-ad-v2

2. Double check what AppType your Azure Bot resource is and make sure your env file is correct. Please update the AppType your env file to SingleTenant and supply your TenantId to communicate with the bot.

3. Another reason might be your bot registered into your tenant (and not the global bot framework). So, you can get the access token by changing the URL to the following (replacing with your tenant id):

https://login.microsoftonline.com/YOUR-TENANT-ID/oauth2/v2.0/token

Thanks, 

Prasad Das

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