Maven - why does running a build of multiple packages result in a different result?

You are observing some weird behaviour because plugin's author didn't pay much attention to maven internals:

private val rootProjectDir: File
  get() = reactorProjects[0].basedir

private fun collectExecFiles(): Set<File> {
 return if (dataFileIncludes == null) {
   setOf(dataFile)
 } else {
   FileUtils.getFiles(rootProjectDir, dataFileIncludes, dataFileExcludes).toSet()
 }
}

Injecting reactorProjects makes sense for @aggregator mojos, because when we are dealing with multi-module project structures and have parent-child relations we need special handling of such cases (for example, there are two mojos in jacoco-maven-plugin: report and report-aggregate). In your case plugin's author is trying to kill two rabbits with single shot, that in your particular case leads to the following:

when you run maven like -pl moduleA -am then when maven executes verify phase of Module B reactor projects are Module A, Module B, plugin tries to pick up exec files from Module A directory and fails: Module A depends on Module B and there are no exec files in Module A directory.