UNet Player prefab cannot be spawned after update to 5.6

I have a NetworkManager and Network Manager HUD components with Player prefab set to Auto Create.
Just an hour ago it was working perfectly in Unity 5.4.1f, now I updated to 5.6.0f and my game simply doesn’t work. The player prefab isn’t spawned when I join the game. It is when I host, but I get an error:

GameObject Player is a prefab, it can’t be spawned. This will cause errors in builds

Still if I try to join the game, the ManagerHud shows that the connection is succesful and is just stuck there, without spawning my player prefab.

Is that a bug in the new version? Or has the way of setting things up changed?

"GameObject Player is a prefab, it can't be spawned. This will cause errors in builds." - Questions & Answers - Unity Discussions there is a similar discussion. I ran into the same issue. I’ve scaled down my project just to a few objects in the scene just to find out what causing the problem. I found that in my case even if change “Player Prefab” to any other gameobject (a simple non prefab dummy object with NetworkIdentity), Unity3d continues to blame the original prefab over simulation restarts until I restart the Editor itself. So yeah, at least the last thing is definitely a bug. Moreover, I can use some other prefabs as a “Player Prefab”, but not the particular one. I’m also curious about any changes (as pointed out in the link above) to the network framework, and whether we should set a prefab to “Player Prefab” field.
I’ve faced the issue on 5.6f3 and tried 5.6p1 with no luck.

See this solution https://forum.unity3d.com/threads/5-6-unet-prefab-linked-gameobjects-within-the-scene.464178/#post-3039735 use a text editor or something and just change the mentioned value to 0.