It looks like the problem comes from having scalafix-core & sbt-scalafix in the same classpath:
https://github.com/scalacenter/sbt-scalafix/blob/2de5eca0bd0f189ef9216759136431aaab25dbff/src/main/scala/scalafix/Versions.scala#L6-L13 shadows https://github.com/scalacenter/scalafix/blob/5d6b2e296c70e1666b91dd9368f7fad81106133e/project/ScalafixBuild.scala#L93-L110. scalacenter/scalafix#1562 triggered this.

FWIW, a hack like does the trick, to favor Versions from scalafix-core over sbt-scalafix considering that:

• sb-scalafix is brought transitively
• order is deterministic https://github.com/sbt/sbt/blob/878250e78ecc6a610b58786d9be7d8dd8b6bc932/main/src/main/scala/sbt/Defaults.scala#L2687

 lazy val plugin = project
   .in(file("plugin"))
   .enablePlugins(ScriptedPlugin)
   .dependsOn(LocalProject("common2_12"), LocalProject("fix2_12") % Test)
   .settings(
     commonSettings,
     description := "find unused code sbt plugin",
     scalapropsSettings,
     scalapropsVersion := "0.9.0",
     addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % _root_.scalafix.sbt.BuildInfo.scalafixVersion),
     scriptedLaunchOpts += "-Dplugin.version=" + version.value,
     scriptedBufferLog := false,
     sbtPlugin := true,
     name := "unused-code-plugin",
     moduleName := "unused-code-plugin",
+    Test / dependencyClasspath := (Test / dependencyClasspath).value.reverse,
   )

By the way, thanks for this fascinating project @xuwei-k! I didn't have a deep look at the implementation, but I was wondering if you considered implementing unusedCode as a scalafix rule itself (which would just collect the data consumed by WarnUnusedCode & RemoveUnusedCode) for more portability? Users would then just need to run scalafix DetectUnusedCode WarnUnusedCode without the need for a separate plugin.