The issue is that autokey-gtk's phrase-editor is not properly inheriting the dark background prescribed by the GNOME theme. The phrase-editor's background-color remains white no matter what the GNOME theme prescribes.
Conflictingly, the autokey-gtk phrase-editor is indeed properly inheriting the caret-color (typing cursor color) from the GMONE theme. The typing-cursor is not "missing"; it is there, but because its color is the same color as the background-color, it is invisible to the human eye.
Until this theme-inheritance bug is fixed in autokey-gtk, a work-around would be to change the caret-color to a color that remains visible on the dark theme you're using. For example, you could change the caret-color to blue.
* {caret-color: blue; }
adding above line in the .css
file of the source file made it blue color

for example to override Yaru-Dark theme
navigate to /usr/share/themes/Yaru-Dark/gtk-3.20/gtk-dark.css
and add the below line under the line @import url("resource:///com/ubuntu/themes/Yaru/3.20/gtk-dark.css");
* {caret-color: blue; }

to apply this line * {caret-color: blue; }
to all the theme files (globally)
just put this line in the file ~/.config/gtk-3.0/gtk.css

reference: https://askubuntu.com/a/1159560/739431