I know your post is old but I just went through this myself and thought I would share what I know.
My ls output was giving me the same thing but only on my partition where I store my data. That partition is an NTFS partition (some call it a "Windows type partition"). The ls command give different colors on a "Windows partition" and that's why I was getting the green highlights. I fixed my problem by adding a line to the bottom of my .bashrc file. The highlights went away and I was left with light blue for directories and green for files. Here's how I fixed it.
Shut down all open terminal emulators
Back up your .bashrc file (go to your home folder and press Ctrl-h to see your hidden / "." files and folders
Edit your .bashrc file
Add the following line to the bottom of .bashrc
export LS_COLORS='ow=01;36;40'
Save your .bashrc file. Some people say you have to run "source ~/.bashrc" to get your changes to take, but I never had to.
Open your terminal emulator and see if the highlights are gone
I know your post is old but I just went through this myself and thought I would share what I know.
My ls output was giving me the same thing but only on my partition where I store my data. That partition is an NTFS partition (some call it a "Windows type partition"). The ls command give different colors on a "Windows partition" and that's why I was getting the green highlights. I fixed my problem by adding a line to the bottom of my .bashrc file. The highlights went away and I was left with light blue for directories and green for files. Here's how I fixed it.
export LS_COLORS='ow=01;36;40'
Hope that helps!