for example, if the build-helper plugin is added to module pom with <source> parameter set as
<source>${project.build.directory}/src</source>
then after idea project creating from this maven project this extra root appears in idea module settings like
${project.build.directory}/src, not resolving to some path.
if you change the <source> attribute value to some path, the above incorrect root is not removed from module.

Issue was resolved