Just wanted to add another data point - I also had a "files in use" warning while trying to install the update for Exchange Server 2016 on Windows Server 2016 a few weeks ago. Defender AV was disabled, and the server was restarted shortly before I started the installation. The update installer warned about these applications in use:
DHCP Client
Message Queueing
Net.Msmq Listener Adapter
Network List Service
Network Location Awareness
nxlog
TCP/IP NetBIOS Helper
Time Broker
Windows Event Log
WinHTTP Web Proxy Auto-Disovery Service
I tried manually stopping some, but they were restarting themselves so I cancelled the Exchange update and restarted the server. After restart I had the same problem as this commenter from a few months ago - all of the Exchange services were still in the Disabled state. After restart I tried the installation again, got the same warning about open applications, ignored it and continued the installation. The installation was successful, but afterwards all the Exchange services were still disabled (again like the above commenter). I manually changed all the services to their original startup type, and we haven't noticed any issues since then.