Computers are being merged with completely non related data. For example they do not have a matching Resource Key, Serial Number, Barcode or any other seemingly obvious data.
There is a task that runs twice a day be default named "NS.Merge Duplicate Resources" this has the ability to cause computers to merge if they have a duplicate Mac address and Ip Address.
This could occur with things like virtual machines in an environment where dhcp is allowing multiple computers to use the same IP address.
Some VPN adapters identify with the same Mac Address and the common home routers could come across as a matching IP.
There may be other scenarios as well.
The scheduled task "NS.Merge Duplicate Resources" runs an SQL stored procedure that is doing the bulk of the work.
The attached file is an updated version of the stored procedure that excludes this scenario.