The jacoco report published by pipeline indicates classes that should have been excluded.
Our build, a multi-module maven build executes jacoco on multiple modules. In the POM, we indicate <exclude> on a number of classes (generated java). When built by maven (command-line), the jacoco report is properly created - excluded files are properly excluded. When we wrapper this build into a jenkinsfile and invoke it via a withMaven(..), the JacocoPublisher kicks in. The jacoco report on the Jenkins job appears to include the excluded files. It looks to me like JacocoPublisher is reinvoking Jacoco-Plugin with default parameters. The Jacoco-Plugin output shows a blank line for 'exclude', which explains why the report has things it should not.
I suspect the easiest solution is to offer a parameter on JacocoPubisher that would pass-through to the Jacoco-Plugin. This would allow people to write Jenkinsfiles, enter the 'excludes' they desire, and Jacoco-Plugin would then run properly.