@backyardheirloomseeds: I have the same issue on our website http://www.beneluxexpat.com. I turned off the debug mode in my wp-config to turn off those notifications.
I am trying to find the source of this problem. But it has to do with the limitation of Godaddy servers. Our server can have a maximum of 250.000 files and we are above it. It all started after we hit the 250.000 files.
I'm going to contact Godaddy within 1 hour and update my post when I know more.