To reproduce:
1) Open '2DBug.rar' project that user attached.
2) Open 'Scene' scene and press play
3) You will notice that in 2D part, left red cube goes right trough blue rectangle while in 3D, right red cube stays on blue rectangle.

There are script attached that removes rigidbodies from those objects on start.

It is expected that 2D cube stays on rectangle, rather than falling trough, since rectangle still has 'Box Collider 2D'.

Disabling and enabling 'Box Collider 2D' on rectangle makes it behave as expected, it seems that disabling 'Rigidbody2D' disables and 'Box Collider 2D' along with it, without showing that in object inspector.