Duplicate sources.list entry

I have noticed the warning:

 W: Duplicate sources.list entry http://ports.ubuntu.com/ubuntu-ports/ trusty/main armhf Packages (/var/lib/apt/lists/ports.ubuntu.com_ubuntu-ports_dists_trusty_main_binary-armhf_Packages)
 W: Duplicate sources.list entry http://ports.ubuntu.com/ubuntu-ports/ trusty/universe armhf Packages (/var/lib/apt/lists/ports.ubuntu.com_ubuntu-ports_dists_trusty_universe_binary-armhf_Packages)
 W: You may want to run apt-get update to correct these problems

In our Saucy and Trusty builds. It seems we have the same archive listing in:

/etc/apt/sources.list and in /etc/apt/sources.list.d/*

This is not blocking anything, but would be nice if we could sort it out so apt doesn't complain.