When I connect my HDMI along with my second monitor and built in display, I get this from my top bar, a weird two-row duplication.
How do I get rid of it?
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It's in fact a weird problem. And maybe you should try to open a bug ticket to the Ubuntu Developers. Despite that, this what I would try:
I've solve many issues regarding Ubuntu using Gnome's Shell Extensions, this is one you should try:
If that doesn't work, you might consider upgrade your version to 18.10.