As always, the solution came up to my mind right after posting the question. It seems that Maven detected that bootstrap-datepicker was depending on bootstrap. I suppose that it included Bootstrap in different version in result - that would explain everything.
However, this is the solution:
<!-- WebJars -->
<dependency>
<groupId>org.webjars</groupId>
<artifactId>webjars-locator</artifactId>
<version>0.1</version>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap-datepicker</artifactId>
<version>1.3.0</version>
<exclusions>
<exclusion>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.webjars</groupId>
<artifactId>bootstrap</artifactId>
<version>3.1.0</version>
</dependency>
Is anybody aware of simple solution to browse /webjars directory structure after the Maven compilation? This would prevent such issues.