[IN THE EDITOR]
Steps to reproduce the issue:
1. Download and open attached project.
2. Open scene named "MainScene".
3. Enter the Play mode.
4. Notice that the "Console" window regularly outputs this message:
[PCG_9744] Test member is 5
5. Let the scene run for several minutes.

Actual result:
After some time the loading process fails and the "Console" window outputs these error messages:

The referenced script on this Behaviour is missing!
UnityEngine.AssetBundleRequest:get_asset()
AssetBundleLoader:OnAssetLoaded(AssetBundleRequest) (at Assets/AssetBundleLoader.cs:82)
<WaitAndLoadAsset>c__Iterator1:MoveNext() (at Assets/AssetBundleLoader.cs:76)
UnityEngine.SetupCoroutine:InvokeMoveNext(IEnumerator, IntPtr)

The referenced script on this Behaviour (Game Object 'TestPrefab') is missing!
UnityEngine.AssetBundleRequest:get_asset()
AssetBundleLoader:OnAssetLoaded(AssetBundleRequest) (at Assets/AssetBundleLoader.cs:82)
<WaitAndLoadAsset>c__Iterator1:MoveNext() (at Assets/AssetBundleLoader.cs:76)
UnityEngine.SetupCoroutine:InvokeMoveNext(IEnumerator, IntPtr)

GameObject (named 'TestPrefab') references runtime script in scene file. Fixing!
UnityEngine.AssetBundleRequest:get_asset()
AssetBundleLoader:OnAssetLoaded(AssetBundleRequest) (at Assets/AssetBundleLoader.cs:82)
<WaitAndLoadAsset>c__Iterator1:MoveNext() (at Assets/AssetBundleLoader.cs:76)
UnityEngine.SetupCoroutine:InvokeMoveNext(IEnumerator, IntPtr)

Expected result:
The loading process should not fail and error messages should not appear.

Reproduced with:
5.3.6p2, 5.4.0f3, 5.5.0a5.

Cannot reproduce with:
5.1.5f1, 5.2.5f1, because the loading process does not work at all.

Note:
With 5.4.0f3 version of Unity the Editor even crashed after some time.

========== OUTPUTING STACK TRACE ==================

0x0000000140134BC2 (Unity) AwakeAndActivateClonedObjects
0x00000001401350A2 (Unity) CollectAndProduceClonedIsland
0x000000014013514B (Unity) CollectAndProduceClonedIsland
0x00000001401356CC (Unity) CloneObject
0x0000000140E8682C (Unity) Object_CUSTOM_Internal_CloneSingle
0x00000000130F0605 (Mono JIT Code) (wrapper managed-to-native) UnityEngine.Object:Internal_CloneSingle (UnityEngine.Object)
0x00000000130F0440 (Mono JIT Code) [C:\buildslave\unity\build\Runtime\Export\UnityEngineObject.cs:164] UnityEngine.Object:Instantiate (UnityEngine.Object)
0x00000000130F00FC (Mono JIT Code) [C:\Users\LocalAccount\Downloads\case_821051-PCG_9744\Assets\AssetBundleLoader.cs:83] AssetBundleLoader:OnAssetLoaded (UnityEngine.AssetBundleRequest)
0x00000000130EF9B2 (Mono JIT Code) [C:\Users\LocalAccount\Downloads\case_821051-PCG_9744\Assets\AssetBundleLoader.cs:76] AssetBundleLoader/<WaitAndLoadAsset>c__Iterator1:MoveNext ()
0x0000000012FED6C8 (Mono JIT Code) [C:\buildslave\unity\build\Runtime\Export\Coroutines.cs:17] UnityEngine.SetupCoroutine:InvokeMoveNext (System.Collections.IEnumerator,intptr)
0x0000000012FED83B (Mono JIT Code) (wrapper runtime-invoke) <Module>:runtime_invoke_void_object_intptr (object,intptr,intptr,intptr)
0x00007FFC4557519B (mono) [c:\buildslave\mono\build\mono\mini\mini.c:4937] mono_jit_runtime_invoke
0x00007FFC454C84FD (mono) [c:\buildslave\mono\build\mono\metadata\object.c:2623] mono_runtime_invoke
0x000000014036020F (Unity) scripting_method_invoke
0x00000001404C432F (Unity) ScriptingInvocation::Invoke
0x000000014033A68E (Unity) Coroutine::InvokeMoveNext
0x000000014033AB45 (Unity) Coroutine::Run
0x0000000140131B05 (Unity) DelayedCallManager::Update
0x0000000140462AA3 (Unity) PlayerLoop
0x0000000140BD2A05 (Unity) Application::UpdateScene
0x0000000140BD3F89 (Unity) Application::UpdateSceneIfNeeded
0x0000000140BDBE54 (Unity) Application::TickTimer
0x0000000140E3D91E (Unity) FindMonoBinaryToUse
0x0000000140E3EF4C (Unity) WinMain
0x00000001415BCA40 (Unity) strnlen
0x00007FFC73D58102 (KERNEL32) BaseThreadInitThunk

========== END OF STACKTRACE ===========

[ON ANDROID]
Use "AndroidTest.apk" file (it is located in the "Builds" folder) to reproduce the same issue. These error messages should be visible:

The referenced script on this Behaviour is missing!
The referenced script on this Behaviour (Game Object 'TestPrefab') is missing!
The file 'none' is corrupted! Remove it and launch unity again!