When I style body links to a specific hover color this color seems to be used also on some of the WordPress toolbar (also known as the front "admin bar") menu links. This is not always desired, because the background color of this bar is quite dark.

If I add this CSS Insert

#wpadminbar a { color: inherit !important; }

then this problem is fixed.

A couple of versions ago theme authors could assume that every element visible on the front was controlled by the theme. This is no longer true when the toolbar is visible (for logged in users who wants this).

If this is a (small) bug I suggest it be fixed so that styling of the body element never affects the WP toobar (#adminbar).

This isn't a theme bug. The styling for this area is created by wordpress. If you look at the source of a page you will find the line

<link rel='stylesheet' id='admin-bar-css'  href='http://yourdomain.com/wp-includes/css/admin-bar.css?ver=20111209' type='text/css' media='all' />

I have no idea how WP decides on these options but if your theme settings conflict wth it, you will have to override the options in this style sheet.