It doesn't cause a site to stop working - it just "looks slightly amiss" if someone views the ssl cert and it says an unexpected site.
It looks like a primary way that subdomains are "revealed" or presented as the main site's ssl cert in "unfortunate random happenings" now is that cpanel creates
www.subdomain.domain.com and this gets its own cert, so eliminating these
www.subdomain entries may help. (have to look into how to do that as cpanel appears to create them automatically).
The actual subdomain.domain.com is covered by *.domain.com but if you have internal-test.domain.com cpanel auto creates
www.internal-test.domain.com which then gets its own cert now which might be presented for domain.com. I think it looks like "something is amiss" if I look at a site and under the ssl cert or site identity it presents the cert subject name as
www.internal-test.domain.com for example.
Another example is a site that uses subdomains or add-on domains for a sub-set of the site that appeals to a different group than the primary audience. It's not a secret, but it looks odd to me. For example if you have a site about high end leather shoes, let's say highfashionshoes.com, and a subdomain is for christmas slippers that goes to one particular small subcategory presented only during the holidays, I think it looks slightly tacky if the ssl cert for the main site suddenly shows
www.christmas-slippers.highfashionshoes.com or christmas-slippers.com as the main site's identity under the ssl cert. It just looks less than premium or slightly tacky/off if that happens.
Granted only nerdy people probably look at the cert. But I will say that there was one web services company that I hesitated to signup with because I did look and their main site showed the ssl cert of a blog site they also ran rather than their main site. Gave me a moment of pause.