I recently wrote an article about an issue that came to the fore a few months ago relating to how the Application Performance Monitoring (APM) feature in SCOM 2016 agent causes IIS Application pools running under the .NET Framework 2.0 runtime to fail. See the article here: http://www.mrchiyo.com/scom-2016-apm-linked-to-iis-application-pool-failures/. It was expected that a definitive fix for this issue would ship with Update rollup 3 for SCOM 2016.
However, update rollup 3 (UR3) for SCOM 2016 was released a few days ago, but it does not appear to have a definitive fix for this issue. See the official update notes here: https://support.microsoft.com/en-us/help/4016126/update-rollup-3-for-system-center-2016-operations-manager
MICROSOFT RECOMMENDED WORKAROUNDS: Instead of a definitive fix, the Microsoft product team has highlighted various deployment scenarios, and workarounds to mitigate or address the problem until a definitive fix for the issue is released. Please review this article for official workaround guidance from Microsoft. https://blogs.technet.microsoft.com/momteam/2017/06/06/update-on-apm-fix-for-agent-crashing-issue-shipped-in-ur3/