Then move up one directory to the install directory and check in the LIB directory for those 2 dlls. If both of them are 8.2, then copy them to the /CMS/bin directory and override the 8.1 dlls. Most likely the upgrade tool couldn't stop the site or access to those files during the upgrade process.
Best thing to do in this case is to stop the site in IIS to make sure no processes are accessing any of the files. This includes having the project open in Visual Studio. Sometimes that alone causes problems.