I have recently deployed a SCOM 2016 solution for a customer. Yesterday, we were informed of an issue where the agent would ‘break’ the IIS Application Pool and this typically presents itself when IIS is restarted.
The issue is linked to APM (Application Performance Monitoring) and this issue occurs even if APM is not enabled in SCOM.
The good news is that there is a very quick and easy workaround to this issue, which only occurs on legacy .NET Framework 2.0/3.5 Application Pools and Kevin Greene (MVP) describes this issue and full background in his blog here.
As pointed out by Kevin, Microsoft have acknowledged this as a bug and plan to provide the permanent fix for this issue in the next Update Rollup (UR3), however until that time, this workaround should resolve the issue.