So when I create a new SubSite for Wordpress, and I try to upload files, it will upload but I won't be able to access those files at the URL.
All existing SubSites work fine, its only new ones.
When I go into the SubSite Settings, it has the wrong file path in there, if I edit it or completely remove it, uploads work fine.
But I couldn't work out where it was getting this from, all the settings seemed to be correct.
Turns out its getting this file path from the Root Site (Site ID: 1 which I don't use so I'd totally forgotten about.) This was wrong because I'd moved the site to a new host but hadn't picked up on this issue because all existing sites worked fine, only when I created a new subsite I noticed the issue.
After I changed the file path in the root site to the correct path, all new site deployments have the correct path and upload files fine.
Just wanted to make anybody else who's racking their brain trying to figure this out aware, and now If encounter the same issue again, I know a search of WPMUDev will help me out.