Redmine

I had an problem this morning where file uploads would not work. I tracked the problem down to the user that was set as the owner of the folder that the files were being saved to. It appears that the folder structure for files is separated by year then month.
For example
files -> 2016-> 01 02 03 04 etc.
Today a new folder was created for December with the folder name 12 but root was assigned as owner and this was causing uploads to fail. After I set the correct owner everything works fine. This problem has never come up before and I am wondering if there is something I need to do to make sure that it doesn't in the future. Has anyone else had this problem and maybe know how to fix it?

Here is my redmine info:
Environment:
Redmine version 3.0.4.stable
Ruby version 1.9.3-p551 (2014-11-13) [x86_64-linux]
Rails version 4.2.3
Environment production
Database adapter Mysql2

Also this is on a Apache 2.4.23 server using Phusion Passenger 5.0.13.