In my case I had in main pom:
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.0.3.RELEASE</version>
</parent>
which includes plugin spring-boot-maven-plugin.
I had to add to main pom to skip it:
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
and then in module with ma Application class:
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<skip>false</skip>
</configuration>
</plugin>