@Leo - Welcome to Microsoft Q&A and thanks for reaching out to us.
Sorry for the inconvenience caused to you.
Have you tried deleting the Managed Application yet? To remove the deny assignment, you need to delete the managed application. If not, try it and then see if it helps deleting the RG, Vnets and subnets.
Please refer to the below document for more information: https://learn.microsoft.com/en-us/azure/azure-resource-manager/managed-applications/overview#managed-resource-group?WT.mc_id=AZ-MVP-5000120
Hope this helps. and please feel free to reach out if you have any further questions.
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