Updating WordPress or plugins causes site issues (due to API, I think)

I have a problem with all of the sites I host on my server. Whenever someone updates WordPress of plugins, I manually have to restart Apache to get things to work properly.

Should the update process clear the APC caches itself, if if so, any ideas what could cause this to not work correctly?

I've checked the latest victim site, there's not caching plugin on this site, for reference,

Topic apc cache updates Wordpress

Category Web

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