Fix duplicate references in scene.mobjects after ReplacementTransform with existing target mobject

manim/scene/scene.py

@@ -553,6 +553,10 @@ def replace(self, old_mobject: Mobject, new_mobject: Mobject) -> None:
         def replace_in_list(
             mobj_list: list[Mobject], old_m: Mobject, new_m: Mobject
         ) -> bool:
+            # Avoid duplicate references to the same object in self.mobjects
+            if new_m in mobj_list:
+                mobj_list.remove(new_m)
+
             # We use breadth-first search because some Mobjects get very deep and
             # we expect top-level elements to be the most common targets for replace.
             for i in range(0, len(mobj_list)):

tests/module/animation/test_transform.py

@@ -0,0 +1,27 @@
+from __future__ import annotations
+
+from manim import Circle, ReplacementTransform, Scene, Square, VGroup
+
+
+def test_no_duplicate_references():
+    scene = Scene()
+    c = Circle()
+    sq = Square()
+    scene.add(c, sq)
+
+    scene.play(ReplacementTransform(c, sq))
+    assert len(scene.mobjects) == 1
+    assert scene.mobjects[0] is sq
+
+
+def test_duplicate_references_in_group():
+    scene = Scene()
+    c = Circle()
+    sq = Square()
+    vg = VGroup(c, sq)
+    scene.add(vg)
+
+    scene.play(ReplacementTransform(c, sq))
+    submobs = vg.submobjects
+    assert len(submobs) == 1
+    assert submobs[0] is sq