Hello,
How are you updating the Windows Updates? Is that by running the Windows Update from Control Panel OR via WSUS?
I wonder if you have Symantec Endpoint Protection 12.1 RU2 (12.1.2015) installed on Windows Server 2012.
I checked my Windows 2012 server and received no Errors. I have installed SEP 12.1.2015 (full feature set) on Windows 2012.
In case you carrying SEPM and WSUS, you still should not have any issues since 12.1 no longer users IIS.
The main problem in the past was having both the SEPM and WSUS being hosted on the default website...if configured this way there can be issues.
There is no inherent incompatability. I do, however, recommend monitoring for performance.
Both SEPM and WSUS will be competing for the same resources (network ports, bandwidth, CPU cycles, hard drive space) while keeping your environment up-to-date. If you have a very large environment and there are any signs that WSUS or SEPM is struggling to keep up with its job, it would be a good idea to move each to a dedicated server. The best admins take stability and security very seriously, and ensure that the tools which look after that (SEPM and WSUS) have plenty of resources to do their job right.
Hope that helps!!