It seems that some applications (none mentioned and none forgotten) create services where the path to the service is written with forward slashes. The migration engine in Windows 10 does not recognize this as a valid path and therefore do not migrate those services and they are thereby missing after upgrade.
The following can be found in the setupact.log (located in C:\Windows\Panther) after upgrading Windows 10 to a new build:
2017-02-07 16:07:42, Info [0x08056f] MIG Start processing unit="Services"
2017-02-07 16:07:42, Warning MIG CAddSystemServicesExpander::ExtractImagePath: Failed to extract file path from APP_Service::ImagePath=["C:/Program files/Vendor/Product/APP_Service.exe"]
The solution is to make sure the application is installing the service with a path that contain backslashes instead of forward slashes.