During the development I have found strange Collider2D behavior in Unity 4.6.0f1 (not sure if it is a 4.6 issue?).
To reproduce a problem I created a separate project and very simple scene with 3 objects (Picture 1). Each object have only Rigidbody2D and BoxCollider2D. The red one have also simple move script (only add force in each direction on keypress).
When all objects are root in the scene hierarchy everything works fine (Picture 2). The problem occurs when those objects have the same parent:
Parent
TestObjectPlayer
TestObject
TestObject
TestObject
Than Colliders 2D stops working (Picture 3). The funny thing is that when I simply during run-time disable the Collider on the Player Object and than enable it again it starts working.