Repro: open a small script in the Web Inspector, so that there is an empty space at the bottom of the viewer (i.e. no vertical scrollbar). The gutter's height should be 100% in this case. Also a small UI tweak: set gutter's min-width to 19px, which is the minimum width to display a breakpoint marker.
Created attachment 84415 [details] Patch
Committed r80348: <http://trac.webkit.org/changeset/80348>