At first let me note, that unfortunately, "Organize Imports" is known to have quite a few issues :-/. People who want to help out with are always welcome! That being said, I could reduce src/test/scala/xitrum/params/ParamsTest.scala to

package xitrum.params

import org.scalatest._
import com.m3.curly.scala._

class ParamsTest extends FlatSpec {
  "foo" should "not bar" in {
    val response: Response = ???
    response
  }
}

and still reproduce the misbehavior you described above. I'll see what I can do to fix this.

Well, I now have a simple example to reproduce this without any external dependencies: Organizing imports on

package com.github.mlangc.experiments

import com.github.mlangc.experiments.test._

package test {
  class Test
}

class Bug {
  None.getOrElse {
    val x: Test = ???
    x
  }
}

results in

package com.github.mlangc.experiments

import com.github.mlangc.experiments.test.Test

import com.mlangc.experiments.Bug.<local Bug>.x

package test {
  class Test
}

class Bug {
  None.getOrElse {
    val x: Test = ???
    x
  }
}

This is fixed by https://github.com/scala-ide/scala-refactoring/pull/88

The fix was merged and will be part of the next IDE release.