To reproduce:
1. Extract the project;
2. Create a Perforce workspace A that points to the project;
3. Open the project in Unity;
4. Configure the Unity Perforce integration to use workspace A;
5. Use workspace A to submit the contents of the Assets and ProjectSettings folders to Perforce;
6. Create another Perforce workspace B that points to the same depot content, and have it point to a different folder on your machine;
7. Use workspace B to check out custom_scriptable_object.asset and custom_scriptable_object.asset.meta;
-Note: Make sure custom_scriptable_object.asset and custom_scriptable_object.asset.meta have 'exclusive checkout' (if not, press right mouse click on files > Change File Type... > Check "Exclusive Checkout");
8. Submit the changes to confirm "Exclusive Checkout"
9. Back in Unity, with workspace A, run this menu command: Custom -> Write Locked File;
10. Notice that "custom_scriptable_object.asset" is not Read-only anymore.

Expected result:
-Unity reports that custom_scriptable_object.asset cannot be checked out.
-Unity does not check out custom_scriptable_object.asset.meta.
-Unity does not write custom_scriptable_object.asset.

Actual result:
-Unity reports that custom_scriptable_object.asset cannot be checked out.
-Unity does check out custom_scriptable_object.asset.meta.
-Unity does write custom_scriptable_object.asset.

Reproduced on versions: 2017.2.2p1, 2017.3.1p4, 2018.1.0b10, 2018.2.0a4.