diff --git a/core-jvm/src/main/scala/coursier/core/package.scala b/core-jvm/src/main/scala/coursier/core/package.scala
index aaf241b9f..3d7851006 100644
--- a/core-jvm/src/main/scala/coursier/core/package.scala
+++ b/core-jvm/src/main/scala/coursier/core/package.scala
@@ -11,7 +11,7 @@ package object core {
                  profileActivation: Option[(String, Activation, Map[String, String]) => Boolean]): Stream[Resolution] = {
 
     val startResolution = Resolution(
-      dependencies, dependencies, Set.empty,
+      dependencies, Set.empty, Set.empty,
       Map.empty, Map.empty,
       filter,
       profileActivation
diff --git a/core/src/main/scala/coursier/core/Resolution.scala b/core/src/main/scala/coursier/core/Resolution.scala
index 4ccabce8f..33c574d6d 100644
--- a/core/src/main/scala/coursier/core/Resolution.scala
+++ b/core/src/main/scala/coursier/core/Resolution.scala
@@ -330,7 +330,7 @@ object Resolution {
     val dependencies0 = dependencies.map(withDefaultScope)
 
     val startResolution = Resolution(
-      dependencies0, dependencies0, Set.empty,
+      dependencies0, Set.empty, Set.empty,
       Map.empty, Map.empty,
       filter,
       profileActivation
@@ -397,7 +397,7 @@ case class Resolution(rootDependencies: Set[Dependency],
    * Returns a tuple made of the conflicting dependencies, and all the dependencies.
    */
   def nextDependenciesAndConflicts: (Seq[Dependency], Seq[Dependency]) = {
-    merge(dependencies ++ transitiveDependencies)
+    merge(rootDependencies ++ dependencies ++ transitiveDependencies)
   }
 
   /**