Seems to be intentional:

> apt (0.7.26~exp8) experimental; urgency=low
> 
>   [ David Kalnischkies ]
>   ...
>   * apt-pkg/contrib/fileutl.cc:
>     - show notice about ignored file instead of being always silent
>     - add a Dir::Ignore-Files-Silently list option to control the notice

So using

sudo apt-get -o dir::ignore-files-silently::="\.save$" update

won't complain. Those .save files seem to come from software-properties-
gtk btw.

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sources are not recognized 
https://bugs.launchpad.net/bugs/611925
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