Before this was not bothering me, but now when website traffic has gone medium i get more and more of these messages in my error.log:
File does not exist:
(13)Permission denied:
What’s funny about that is that 90% of the files that are being tagged as permission denied do not actually exist on my server.
How to debug this situation or what usually causes this?
Do not worry about this, it is fairly common. Most likely it is because the web browser is requesting the favicon (that little icon you see on your browser’s title bar) for your website but it does not exist. Unless your users start complaining about broken links I wouldn’t worry about it.