It looks like a newer GtkSourceView Common (libgtksourceview-3.0-common_3.14.1-1_all) does not fix this issue. It affects all themes except for Classic (which doesn't specify line number colors).
Building it on Debian Jessie against libgtksourceview-3.0-dev in version 3.14.1-1 fixes this bug. Maybe investigating the version of libtgtksourceview in our repositories will find the problem?
It looks like a newer GtkSourceView Common (libgtksourcevi ew-3.0- common_ 3.14.1- 1_all) does not fix this issue. It affects all themes except for Classic (which doesn't specify line number colors).