Steps to reproduce:
1. Open the attached project (ownCloud)
2. Open the Assets/scene_graveyard.unity scene
3. Select the scene_graveyard->World->FOREST->Vegetation->Trees->tree_sml_2->content->tree_sml_2 prefab in the Hierarchy
4. Press "Apply" in the Inspector
5. Observe that applying the prefab takes too much time

Expected result: Applying the prefab should take a moment
Actual result: Applying the prefab takes too much time

Note:
Unable to test with 5.4
Unable to test with 2017.1
Physics2D.SendContactCallbacks takes too much time

Reproduced with: 5.6.0f3
Not reproduced with: 5.5.3p1