Here we have 2 issues related to sub-domains added as regular sub-servers when the first level domain is present on the same server. As you know virtualmin add all subdomains to the first level domain's zone. But it also add NS records for every subdomain which then brakes the subdomains and they did not resolve because of that. Also it adds additional SPF record but it shouldn't.
The second issue is: is you have test.domain.com and somethingtest.domain.com
note that the "test.domain.com" at the end is the same on the two domains.
and you try to delete "test.domain.com" it deletes also "somethingtest.domain.com"