.htaccess can cause issues if not setup properly. You can learn about that file here.
You could try removing the .htaccess file and see if that resolves the issue and then start with fresh. As far "content file" and scripting issues, code and scripts can cause website problems when not implemented properly. All that would have to be reviewed to see what is going on.
As long as the servers/hosting are operating as they should, website owners are responsible for the formatting, setup and configuration of the files they create and upload, right? I would recommend that you to seek out a professional to help you review what you have in place troubleshoot what may be causing the problem.