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Is it bad that the root folder directory is being assigned to the web root (public_html) folder instead of its own domain folder within the web root?

The current site I'm working on gets random inconsistent 503 errors and just crashes for the next few minutes. Noticed that in the file manager instead of there being a folder for the domain itself, it is just dumped directly into the webroot folder, the public_html. Could this be an issue or at least part of the issue?

That is not uncommon. This could be caused by things like lack of memory, storage space or even the server/site getting overloaded with requests.

I would try increasing memory on WordPress first and checking storage space. As well, if you can see the server logs they may give you a direct answer to the cause.

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