I do not know much about your situation, so I can only give very vague recommendations. I think this breaks down into two areas:
- Generic web hosting concerns
You might also want to look into:
Course size plugin. Not a perfect measurement, but it can help you identify outlier courses.
- Are you saving a lot of automated course backups?
What are the file size limits for your site, courses,
and individual activities? https://docs.moodle.org/37/en/File_upload_size
- Are any of your database tables particularly large? Are you using any custom plugins that are misbehaving? I had a plugin that was writing millions of lines of event records to mdl_logstore_standard_log, and it turned out to be a pretty quick and reasonable fix once I showed it to my developer.
These are just a few things that I've encountered over the years - not an exhaustive list, by any means!