Application started giving error all of a sudden "Server Error in '/' Application." - The process can not access the dll file because it is being used by another process

Hello Experts,

I have server which is hosting more than 40 public facing websites of my customer. All are running on HTTPS.

One of those applications suddenly started giving following error while accessing it.

This is an intermittent problem.. Sometimes users is able to access the website and the next second he gets the following error. And when refreshes the page it works again. 

I have already cleared the Temporary ASP.Net folder twice but issue persists.

This application was working perfectly till yesterday.

I am seeing 1000s of ASP.Net errors related to this application in Event Viewer Yesterday..

Few Details about the application and environment.

Server :  Windows Server 2008 R2

IIS : IIS 7.5

Application pool : Framework 4.0 (Integrated Mode)

Allow32bit Applications : False.

A custom dll has been registered as the background service and it was working fine till yesterday.

Websites is accessed publicly. Problem is intermittent.

Error while accessing the application 

Server Error in '/' Application.

The process cannot access the file 'C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Temporary ASP.NET Files\root\9ad5bc67\f782f20\AppFoundation\Areas\Audits\Cliet.ContractorManagement.Actions.Contracts.dll' because it is being used by another process.

Description: An unhandled exception occurred during the execution of the current web request. Please review the stack trace for more information about the error and where it originated in the code. 

Exception Details: System.IO.IOException: The process cannot access the file 'C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Temporary ASP.NET Files\root\9ad5bc67\f782f20\AppFoundation\Areas\Audits\Cliet.ContractorManagement.Actions.Contracts.dll' because it is being used by another process.

Source Error: 

Stack Trace: 

Version Information: Microsoft .NET Framework Version:4.0.30319; ASP.NET Version:4.0.30319.34237

Warnings found in Event Viewer.

Event code: 3005
Event message: An unhandled exception has occurred.
Event time: 5/18/2015 7:11:27 AM
Event time (UTC): 5/18/2015 5:11:27 AM
Event ID: 5df62c0c72284b80a103c945bb3effde
Event sequence: 2
Event occurrence: 1
Event detail code: 0

Application information:
Application domain: /LM/W3SVC/15/ROOT-224-130763994875417186
Trust level:
Application Virtual Path: /
Application Path: D:\Inetpub\wwwroot\contra.cliet.com - E604120\
Machine name: W8102

Process information:
Process ID: 2400
Process name: w3wp.exe
Account name: IIS APPPOOL\contra.cliet.com - E604120

Exception information:
Exception type: InvalidOperationException
Exception message: The pre-application start initialization method RegisterAreaAssemblies on type AppFoundation.Web.App_Start.AreaConfig threw an exception with the following error message: The type initializer for 'AppFoundation.Web.MvcApplication' threw an exception..
at System.Web.Compilation.BuildManager.InvokePreStartInitMethodsCore(ICollection`1 methods, Func`1 setHostingEnvironmentCultures)
at System.Web.Compilation.BuildManager.InvokePreStartInitMethods(ICollection`1 methods)
at System.Web.Compilation.BuildManager.CallPreStartInitMethods(String preStartInitListPath, Boolean& isRefAssemblyLoaded)
at System.Web.Compilation.BuildManager.ExecutePreAppStart()
at System.Web.Hosting.HostingEnvironment.Initialize(ApplicationManager appManager, IApplicationHost appHost, IConfigMapPathFactory configMapPathFactory, HostingEnvironmentParameters hostingParameters, PolicyLevel policyLevel, Exception appDomainCreationException)

The type initializer for 'AppFoundation.Web.MvcApplication' threw an exception.
at AppFoundation.Web.App_Start.AreaConfig.RegisterAreaAssemblies()

Failed to load controller assembly "D:\Inetpub\wwwroot\contra.cliet.com - E604120\Areas\Audits\bin\cliet.ContractorManagement.Actions.Contracts.dll": The process cannot access the file 'C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Temporary ASP.NET Files\root\9ad5bc67\f782f20\AppFoundation\Areas\Audits\cliet.ContractorManagement.Actions.Contracts.dll' because it is being used by another process.
at AppFoundation.Web.Runtime.AppFoundationRuntime..ctor()
at AppFoundation.Web.MvcApplication..cctor()

The process cannot access the file 'C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Temporary ASP.NET Files\root\9ad5bc67\f782f20\AppFoundation\Areas\Audits\cliet.ContractorManagement.Actions.Contracts.dll' because it is being used by another process.
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.IO.File.InternalCopy(String sourceFileName, String destFileName, Boolean overwrite, Boolean checkHost)
at AppFoundation.Web.Runtime.AppFoundationRuntime.GetControllerAssemblies()

Request information:
Request URL: https://conta.cliet.com:443/Areas/Issues/Scripts/html2canvas.js
Request path: /Areas/Issues/Scripts/html2canvas.js
User host address: 160.221.251.12
User:
Is authenticated: False
Authentication Type:
Thread account name: IIS APPPOOL\contra.cliet.com - E604120

Thread information:
Thread ID: 77
Thread account name: IIS APPPOOL\contra.cliet.com - E604120
Is impersonating: False
Stack trace: at System.Web.Compilation.BuildManager.InvokePreStartInitMethodsCore(ICollection`1 methods, Func`1 setHostingEnvironmentCultures)
at System.Web.Compilation.BuildManager.InvokePreStartInitMethods(ICollection`1 methods)
at System.Web.Compilation.BuildManager.CallPreStartInitMethods(String preStartInitListPath, Boolean& isRefAssemblyLoaded)
at System.Web.Compilation.BuildManager.ExecutePreAppStart()
at System.Web.Hosting.HostingEnvironment.Initialize(ApplicationManager appManager, IApplicationHost appHost, IConfigMapPathFactory configMapPathFactory, HostingEnvironmentParameters hostingParameters, PolicyLevel policyLevel, Exception appDomainCreationException)


Custom event details: