The EMS installation includes installation of Microsoft Visual C++ (VC) 2015. If the server already has a newer version of VC installed, the installation fails. See VC++ 2015 Redistributable installation returns error 1638 when newer version already installed.
If you have a version of VC installed on your server that is newer than 2015, uninstall VC before installing EMS.
When managing more than 5000 endpoints, install SQL Server Enterprise instead of SQL Server Express, which is installed with EMS by default. Otherwise, you may experience database deadlocks. The minimum SQL Server version that FortiClient EMS supports is 2014. It is recommended to use SQL Server 2017 or a later version. See the FortiClient EMS Administration Guide.