The menu bubbles spawned from elements on the panel seems to be shifted to the right that it affects the UX.
Although screenshot shows Dash to Panel in action, I must also describe that this issue also persists when I disabled panel-related extensions.
If you report a bug or ask a question, please include the following information as required:
pkg-config --modversion gtk+-3.0)appindicator or an an extension element

i can confirm this issue with GTK+ 3.24.1 and GNOME 3.30.1

Normal behaviour (Adapta theme):

I have also tried to use old version until v20180311 and the same issue appears. Could be the bring-up to Gnome 3.30 that introduced this issue.
It's an old problem, at least it was in gnome 3.28
this works:
.popup-menu-boxpointer {
-arrow-border-radius: 4px;
-arrow-base: 48px;
}
Wow, I had never expected that's the cause. Thanks for finding out the solution!
I'll push the fixes soon.
Most helpful comment
this works: