This is essentially a clone of
MDL-64865 where this was originally raised. That tracker turned into a task to add more logging to help diagnose the issue but didn't identify or fix the real root cause.
There might be more that one set of symptoms and / or bugs, what we have seen in a couple clients:
1) some selected auth plugins get randomly disabled. It is usually saml but this is likely observer bias as basically everyone uses saml. We've seen it with other auth types
2) on some occasions all plugins are disabled across the board completely