Unity serialization problem "deleted gameobject"

Without any apparent reason my unity project stopped working correctly. Everytime I try to switch scene with

Application.LoadLevelAsync (levelId);

or

Application.LoadLevel (levelId);

I can’t click any object in the scene and the hierarchy shows “deleted gameobject” on every single object:

the debugging log shows a lot of spamming of the following:

Unloading 0 Unused Serialized files
(Serialized files now loaded: 0)
UnloadTime: 0.549058 ms System memory
in use before: 36.6 MB. System memory
in use after: 36.6 MB.

Unloading 1 unused Assets to reduce
memory usage. Loaded Objects now:
1280. Total: 0.568947 ms (FindLiveObjects: 0.042188 ms
CreateObjectMapping: 0.023505 ms
MarkObjects: 0.489692 ms
DeleteObjects: 0.012958 ms)

Unloading 0 Unused Serialized files
(Serialized files now loaded: 0)
UnloadTime: 0.552674 ms System memory
in use before: 36.6 MB. System memory
in use after: 36.6 MB.

Unloading 1 unused Assets to reduce
memory usage. Loaded Objects now:
1286. Total: 0.486377 ms (FindLiveObjects: 0.037970 ms
CreateObjectMapping: 0.021094 ms
MarkObjects: 0.413752 ms
DeleteObjects: 0.013259 ms)

Unloading 0 Unused Serialized files
(Serialized files now loaded: 0)
UnloadTime: 0.597575 ms System memory
in use before: 36.6 MB. System memory
in use after: 36.6 MB.

Unloading 1 unused Assets to reduce
memory usage. Loaded Objects now:
1292. Total: 0.582809 ms (FindLiveObjects: 0.042791 ms
CreateObjectMapping: 0.021395 ms
MarkObjects: 0.514704 ms
DeleteObjects: 0.003616 ms)

Unloading 0 Unused Serialized files
(Serialized files now loaded: 0)
UnloadTime: 0.533086 ms System memory
in use before: 36.6 MB. System memory
in use after: 36.7 MB.

Unloading 1 unused Assets to reduce
memory usage. Loaded Objects now:
1298. Total: 0.547551 ms (FindLiveObjects: 0.040380 ms
CreateObjectMapping: 0.022601 ms
MarkObjects: 0.471310 ms
DeleteObjects: 0.012958 ms)

Is this a bug in Unity?
I’m using Unity 5

Maybe you limit the amount for prefab to Instantiate and Instantiate the object on update?