Organize imports can remove hidden imports. This can cause compilation errors, if the now non-hidden import is ambiguous. For example this code:

package com.example.actors

import My._
import akka.actor.{ ActorRef =>_, _ }

object Test {
  val sys: ActorSystem = ???
  val ref: ActorRef = ???
}

object My {
  trait ActorRef {
    def foo: Int
  }
}

Will be the following (invalid) code after Ctrl+Shift+O (because ActorRef is now ambiguous):

package com.example.actors

import My._
import akka.actor._

object Test {
  val sys: ActorSystem = ???
  val ref: ActorRef = ???
}

object My {
  trait ActorRef {
    def foo: Int
  }
}

Scala IDE version: 4.4.0-rc2-2016-03-25T09:34:01Z-Typesafe
org.scala-ide.sdt.feature.feature.group version: 4.4.0.v-2_11-201603241805-190ee32