At the start it might create confusion for you but let me explain the things in easy way. While running sonar-scanner, sonar-analyzer(compute engine) do the analysis based on configuration provided in properties file. Analyzer will only fail if it finds problem with infra like issue related with plugins, DB etc and other dependency stuff. Now coming to your question that there is lot of issues(E rating) so now after analysation has been done, there is a concept of quality gate in sonarqube through which you can set the criteria which will help to fail or pass the quality gate of your project like in your case you can define if E rating then fail. So while using CI tools like jenkins you can use the plugin that if quality gates failed then jenkins job will be failed even if the analysis is successful.
Oops i wrote a long story but I hope it helps.