Turns out the theme doesn't support this version of GTK. A Solution would be to override the window close CSS for your theme. Navigate to your theme folder and change .window-close to the following.
Folder Location:
/usr/share/themes/YOUR THEME NAME/gnome-shell/gnome-shell.css
Replace with this:
.window-close {
height: 32px; width: 32px;
background-color: transparent;
border-radius: 0;
border: none;
box-shadow: none;
color: transparent;
-shell-close-overlap: 16px;
-st-background-image-shadow: 0 1px 2px rgba(0, 0, 0, 0.28);
background-image: url("assets/window-close.svg");
background-size: 32px;
}
Source:
https://forum.manjaro.org/t/solved-glitch-on-gnome-activities-overview/85485