There have been recent changes to the NotEmptyUriPrefixMatcher class, according to this ticket: https://jira.magnolia-cms.com/browse/MULTISITE-80

Since then, this class doesn't do anymore what its name (NotEmptyUriPrefixMatcher) suggests, because it will also match sites that have an empty URIPrefix.

The description of the rule "domain-and-uri-prefix-not-empty" says: Domain and not empty uri prefix (subsites)

So you cannot configure subsites anymore, this is a very critical issue, please fix this asap.

(there is only one workaround atm: order the subsite above the mainsite in the site definitions, and hope that the order is never reversed during matchin by whatever mechanism)