Yes this happens to me as well and no I don't know the root cause. However I don't remember having to restart the apppool to make it works - just refresh the page is enough.

As a measure of preventative - make sure the Apps folder has all correct and up to date files.

We've already tried that approach of refreshing the page and clearing the browser cache but to  no avail. We've also compared the Apps folder files from a working to a non-working and it give us an identical results.

I have different pop-up message now about view that cannot be located and even restarting the application service isn't working anymore. Any advise on how to fix this issue? 

Specified view 'List' can not be located in 'Organization' app -- Commerce Manager - Customer Management - Organization.

Specified view 'List' can not be located in 'Contact' app -- Commerce Manager - Customer Management - Organization.

Error logs: 

Error Number:121,State:0,Class:20
2017-11-22 01:00:38,074 [101] ERROR EPiServer.Find.Cms.ContentEventIndexer: An exception occurred in 'IndexPageQueue'. System.Data.SqlClient.SqlException (0x80131904): A transport-level error has occurred when receiving results from the server. (provider: Session Provider, error: 19 - Physical connection is not usable)
at System.Data.SqlClient.SqlConnection.OnError(SqlException exception, Boolean breakConnection, Action`1 wrapCloseInAction)
at System.Data.SqlClient.SqlInternalConnection.OnError(SqlException exception, Boolean breakConnection, Action`1 wrapCloseInAction)
at System.Data.SqlClient.TdsParser.ThrowExceptionAndWarning(TdsParserStateObject stateObj, Boolean callerHasConnectionLock, Boolean asyncClose)
at System.Data.SqlClient.TdsParserStateObject.ReadSniError(TdsParserStateObject stateObj, UInt32 error)
at System.Data.SqlClient.TdsParserStateObject.ReadSniSyncOverAsync()
at System.Data.SqlClient.TdsParserStateObject.TryReadNetworkPacket()
at System.Data.SqlClient.TdsParserStateObject.TryPrepareBuffer()
at System.Data.SqlClient.TdsParserStateObject.TryReadByte(Byte& value)
at System.Data.SqlClient.TdsParser.TryRun(RunBehavior runBehavior, SqlCommand cmdHandler, SqlDataReader dataStream, BulkCopySimpleResultSet bulkCopyHandler, TdsParserStateObject stateObj, Boolean& dataReady)
at System.Data.SqlClient.SqlDataReader.TryConsumeMetaData()
at System.Data.SqlClient.SqlDataReader.get_MetaData()
at System.Data.SqlClient.SqlCommand.FinishExecuteReader(SqlDataReader ds, RunBehavior runBehavior, String resetOptionsString, Boolean isInternal, Boolean forDescribeParameterEncryption)
at System.Data.SqlClient.SqlCommand.RunExecuteReaderTds(CommandBehavior cmdBehavior, RunBehavior runBehavior, Boolean returnStream, Boolean async, Int32 timeout, Task& task, Boolean asyncWrite, Boolean inRetry, SqlDataReader ds, Boolean describeParameterEncryptionRequest)
at System.Data.SqlClient.SqlCommand.RunExecuteReader(CommandBehavior cmdBehavior, RunBehavior runBehavior, Boolean returnStream, String method, TaskCompletionSource`1 completion, Int32 timeout, Task& task, Boolean& usedCache, Boolean asyncWrite, Boolean inRetry)
at System.Data.SqlClient.SqlCommand.RunExecuteReader(CommandBehavior cmdBehavior, RunBehavior runBehavior, Boolean returnStream, String method)
at System.Data.SqlClient.SqlCommand.ExecuteReader(CommandBehavior behavior, String method)
at System.Data.SqlClient.SqlCommand.ExecuteReader()
at EPiServer.Find.Cms.ContentChangedEventStore.<>c__DisplayClass12_0.<LoadItems>b__0(SqlConnection con)
at EPiServer.Find.Cms.ContentChangedEventStore.SqlConnect(Action`1 action)
at EPiServer.Find.Cms.ContentChangedEventStore.LoadItems(String spName, IEnumerable`1 parameters)
at EPiServer.Find.Cms.ContentChangedEventStore.LoadItems(Int32 numerOfItems)
at EPiServer.Find.Cms.ContentEventIndexer.IndexPageQueue()

Error Number:-1,State:0,Class:20
2017-11-22 15:10:54,824 [1] ERROR EPiServer.Personalization.visitorGroups.visitorGroupRole: Unable load criterion of type 'xxx.Business.Criterea.CustomerGroupCriteria, xxx.Business'
System.IO.FileNotFoundException: Could not load file or assembly 'xxx.Business' or one of its dependencies. The system cannot find the file specified.
File name: 'xxx.Business'
at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.Assembly.Load(AssemblyName assemblyRef)
at EPiServer.Data.Dynamic.TypeResolver.<>c__DisplayClass12_1.<ResolveType>b__0(AssemblyName assemblyName)
at System.TypeNameParser.ResolveAssembly(String asmName, Func`2 assemblyResolver, Boolean throwOnError, StackCrawlMark& stackMark)
at System.TypeNameParser.ConstructType(Func`2 assemblyResolver, Func`4 typeResolver, Boolean throwOnError, Boolean ignoreCase, StackCrawlMark& stackMark)
at System.TypeNameParser.GetType(String typeName, Func`2 assemblyResolver, Func`4 typeResolver, Boolean throwOnError, Boolean ignoreCase, StackCrawlMark& stackMark)
at System.Type.GetType(String typeName, Func`2 assemblyResolver, Func`4 typeResolver, Boolean throwOnError, Boolean ignoreCase)
at EPiServer.Data.Dynamic.TypeResolver.ResolveType(String typeName, Boolean throwOnError, FallbackTypeResolver fallbackResolver)
at EPiServer.Data.Dynamic.TypeResolver.<>c__DisplayClass10_0.<GetType>b__0(String typeNameKey)
at System.Collections.Concurrent.ConcurrentDictionary`2.GetOrAdd(TKey key, Func`2 valueFactory)
at EPiServer.Data.Dynamic.TypeResolver.GetType(String typeName, Boolean throwOnError)
at EPiServer.Personalization.visitorGroups.visitorGroupRole.CreateCriterion(visitorGroupCriterion visitorGroupCriterion)

WRN: Assembly binding logging is turned OFF.
To enable assembly bind failure logging, set the registry value [HKLM\Software\Microsoft\Fusion!EnableLog] (DWORD) to 1.
Note: There is some performance penalty associated with assembly bind failure logging.
To turn this feature off, remove the registry value [HKLM\Software\Microsoft\Fusion!EnableLog].

System.IO.FileNotFoundException: Could not load file or assembly 'xxx.Business' or one of its dependencies. The system cannot find the file specified.
File name: 'xxx.Business'
at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.Assembly.Load(AssemblyName assemblyRef)
at EPiServer.Data.Dynamic.TypeResolver.<>c__DisplayClass12_1.<ResolveType>b__0(AssemblyName assemblyName)
at System.TypeNameParser.ResolveAssembly(String asmName, Func`2 assemblyResolver, Boolean throwOnError, StackCrawlMark& stackMark)
at System.TypeNameParser.ConstructType(Func`2 assemblyResolver, Func`4 typeResolver, Boolean throwOnError, Boolean ignoreCase, StackCrawlMark& stackMark)
at System.TypeNameParser.GetType(String typeName, Func`2 assemblyResolver, Func`4 typeResolver, Boolean throwOnError, Boolean ignoreCase, StackCrawlMark& stackMark)
at System.Type.GetType(String typeName, Func`2 assemblyResolver, Func`4 typeResolver, Boolean throwOnError, Boolean ignoreCase)
at EPiServer.Data.Dynamic.TypeResolver.ResolveType(String typeName, Boolean throwOnError, FallbackTypeResolver fallbackResolver)
at EPiServer.Data.Dynamic.TypeResolver.<>c__DisplayClass10_0.<GetType>b__0(String typeNameKey)
at System.Collections.Concurrent.ConcurrentDictionary`2.GetOrAdd(TKey key, Func`2 valueFactory)
at EPiServer.Data.Dynamic.TypeResolver.GetType(String typeName, Boolean throwOnError)
at EPiServer.Personalization.visitorGroups.visitorGroupRole.CreateCriterion(visitorGroupCriterion visitorGroupCriterion)

WRN: Assembly binding logging is turned OFF.
To enable assembly bind failure logging, set the registry value [HKLM\Software\Microsoft\Fusion!EnableLog] (DWORD) to 1.
Note: There is some performance penalty associated with assembly bind failure logging.
To turn this feature off, remove the registry value [HKLM\Software\Microsoft\Fusion!EnableLog].

2017-11-22 15:12:50,079 [6] ERROR ASP.global_asax: Backend encountered unhandled error.
System.Web.HttpException (0x80004005): Request timed out.
System.Web.HttpException (0x80004005): Request timed out.
2017-11-22 15:12:50,098 [6] ERROR EPiServer.Global: 1.2.5 Unhandled exception in ASP.NET
System.Web.HttpException (0x80004005): Request timed out.
System.Web.HttpException (0x80004005): Request timed out.

Any further clues on this ?

Any update?

Based on the information that was provided to me, from our Product Development Team, it seems that hitting F5 on the browser/ restarting IIS fixes the issue. We do not know the root cause of the issue but believe that it may be caused as a result of  having a new build on CM project (code change/modify)

The commerce team does not have any plan to fix it in near future as Epi Commerce plans to eventually replace the Commerce Manager UI with a new improved CSR-UI this year. You will be able to migrate to this new CSR-UI management page. 

Hope this helps