As you know, some of the components such as Management Studio (SSMS) and Configuration Manager are shared components of SQL Server instances and they are upgraded when an in-place upgrade is performed. However, they are not supposed to get upgraded with Side-by-side upgrade unless a certain criteria is met.
In-place and Side-by-side upgrades
In-place upgrades refers an installation of newer version of SQL Server that replaces an existing instance of SQL Server completely, including shared components. The key advantage with this is lesser requirements for additional hardware resources and the key disadvantage is incapability of rolling back at a failure of an installation. Side-by-side upgrades refers an installation of newer version of SQL Server as a new instance without replacing the older version of SQL Server installed. This is the most safest way of upgrading a system because it reduces the risk associated with upgrades leaving the original system in place and intact. However, there are few disadvantages with this, such as copying user defined databases manually, configuring security and configuring jobs used manually.
Side-by-side upgrades does not suppose to replace shared components of older version installed. However a replacement can be happened if the major build number of old instance and the major build number of the new instance are identical. This condition is rare to be occurred but this has been seen with SQL Server 2008 and 2008 R2. If you perform an installation of SQL Server 2008 R2 (version is 10.50) as a side-by-side upgrade for SQL Server 2008 (version is 10.00), though it is not an in-place upgrade, new installation will replace all shared components of SQL Server 2008 instance.
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