Steps to reproduce:
1. Open attached project
2. Open "Test" scene
3. Select Capsule gameObject in hierarchy
4. Check Rigidbody constraints check-boxes: Freeze rotation X and Z axis
5. Drag and drop Capsule gameobject to Project folder in order to create prefab

Results: Capsule Rigidbody constraints' values are being lost when you create prefab of gameObject with X and Z rotation axis freezed

Note: repro video in last edit

You can also reproduce by disabling the GameObject, that will reset the Constraints as well.

Reproduced with: 5.5.0b4, 5.5.0b8
Does not reproduces with: 5.5.0b3, 5.4.2f1