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I'm very new to azure so assume Im just missing something but it feel like the error is saying I can't create the certificte before the container app but I also can't create the container app before the certifacte so Im a bit lost

This looks very similar to an issue I reported to the Container Apps team: https://github.com/microsoft/azure-container-apps/issues/525

Ah yes I hit the same issue you reported when trying to set the custom domain in the managed environment. Thanks for sharing! I'll keep an eye on this issue