"This is not good, we have to do this ourselves". And in the end it costs way more, and you end up with an inferiour solution because it's not your core business, and nobody really has any time to work on it.
Very sad really.
The first thing to ask is exactly what you asked here. I can't upvote this enough.
Another one I remember was when some new configuration key was needed and prevented one of the components from starting (took ~2 hours to find what it was).
It doesn't happen often, don't worry that much though, gitlab omnibus works well, but is hard to investigate/fix because it's huge and not a tech stack we do understand well since we mostly use gitlab-ctl commands, so when something goes wrong it's hard
A server is more likely to go belly-up by accident than the presumably redundant GitHub infrastructure, but its life is much less interesting.