While working with Commerce Server 2009 and SharePoint 2010, I was facing this strange issue while running the SharePoint Configuration wizard more than once
Error was:
An unexpected error has occurred. Error message is: The Process cannot access the file
'[drive]:\users\....\AppData\Local\Temp2\Microsoft.Commerce.Portal.Common.dll' because it is being used by another process
Solution
After some search on the google / bing I found a link on msdn CS forums and solved the issue
Original link is : CS MSDN Forums
Error got resolved when I retracted and removed all Commerce related wsp from the SharePoint
When you go to Central Administration > System Settings > Manage Farm Solutions >
If you find any Commerce related wsp there like Commerce Web Parts, remove them and after iisreset try running Commerce SharePoint Configuration wizard again
I hope this helps some one J