See problem described here:
https://confluence.atlassian.com/display/CLOVERKB/Multi-module+Maven+build+on+Bamboo+with+Clover+history+reports

Bamboo uses default '-Dmaven.clover.historyDir=.cloverhistory' location, which is relative and build fails for sub-modules. Users are not able to override this setting (if they define the property in 'Goals' field in 'Maven Task' configuration, the mvn command is executed with two options - one from user and one from Bamboo).

Instead of this Bamboo shall explicitly use the absolute path pointing to a workspace root, e.g.:

-Dmaven.clover.historyDir=${bamboo.build.working.directory}/.cloverhistory

Affects all Bamboo versions.