I came across the same problem on my VDS recently. I was running CentOS with CloudLinux (LVE) and it turned out that CloudLinux was at fault.
Cloud Linux limits resources available to the account so if you get more visitors and resources end, you would get 500 errors.
My solution is to disable any limits set in LVE, so when one website gets a lot of traffic, the whole site might slow down, but it will not give 500 errors.
Kind Regards
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