For anyone else who stumbles across this it looks like my issue was resolved by making sure these are in place which I pulled from the examples given in the linkerd gitops documentation - GitHub - linkerd/linkerd-examples: Examples of how to configure and run linkerd
ignoreDifferences:
- kind: Secret
name: linkerd-proxy-injector-k8s-tls
jsonPointers:
- /data/tls.crt
- /data/tls.key
- kind: Secret
name: linkerd-sp-validator-k8s-tls
jsonPointers:
- /data/tls.crt
- /data/tls.key
- kind: Secret
name: linkerd-policy-validator-k8s-tls
jsonPointers:
- /data/tls.crt
- /data/tls.key
- group: admissionregistration.k8s.io/
kind: MutatingWebhookConfiguration
name: linkerd-proxy-injector-webhook-config
jsonPointers:
- /webhooks
- group: admissionregistration.k8s.io/
kind: ValidatingWebhookConfiguration
name: linkerd-sp-validator-webhook-config
jsonPointers:
- /webhooks
- group: admissionregistration.k8s.io/
kind: ValidatingWebhookConfiguration
name: linkerd-policy-validator-webhook-config
jsonPointers:
- /webhooks