Did you change your DNS nameservers? Your uploading to one place but its still calling on another??
That would explain why some users could get on the site and others couldnt.
New DNS's have to propagate like a new domain. Sometimes it gets wacky when it bounces around. calling on the DB from one server and files from the other
If you updated the proper DNS stuff then your users can clear the DNS for your site on their computers.
This problem should self correct though, it could be a PITA for some users.
If this is happening, it would explain your 404 error on a file you swear is there. haha
I've had issues with it myself over the years. LOL