Comment 4 for bug 1768264

This is typically because of how the theme is drawn.

If you look here: https://bazaar.launchpad.net/~gnome-terminator/terminator/gtk3/files/head:/terminatorlib/themes/

You can see the overrides in place to make Terminator play nice with some themes that do funky things.

But your particular problem /should/ have been fixed by:
https://bazaar.launchpad.net/~gnome-terminator/terminator/gtk3/view/head:/terminatorlib/terminator.py#L454

That should select the background color of your theme, and ensure that the pane handle is drawn with it.

Try attaching a screenshot and let me know what gtk3 theme you use. That might give me more of a clue.