Probably this is not error of ’Network Proxy Preferences', but I'm not sure what component is related to this bug.

Open 'Network Proxy Preferences' and select the 'Ignored Hosts' tab. Add a couple of hostnames to the list then close the window. Open a new shell and type "echo $no_proxy". Here I pasted mine.

$ echo $no_proxy 
localhost,127.0.0.0/8,*.local,
$

As shown above, it has a trailing comma. I checked /system/http_proxy/ignore_hosts with gconf-editor, but it was correctly configured ( "[localhost,127.0.0.0/8,*.local]" ).

Usually it does not cause any problem, but wget is affected. When $no_proxy has a trailing comma, wget does not use proxy to connect to any hosts, even if they are not listed in the $no_proxy. When I gave $no_proxy without the comma to wget manually, it perfectly worked.