A cloud-based identity and access management service for securing user authentication and resource access
Thank you for posting your question in Microsoft Q&A.
Usually there are some applications that get's created in directory due to some tools like AD connect.
These applications can only be deleted using the same tool.
Using PowerShell we have pull the applications which are available in your directory.
Post that we can try to delete them using PowerShell itself.
Let's try to connect offline to troubleshoot this issue further.
Please send us an email on azcommunity [at] microsoft [dot] com with Sub - Attn: Sandeg and following details in the email body:
Link to this thread/post
We can connect offline and discuss further on this.