Distorted indicators and non-transparent background
After shifting to gnome-41.1 in manjaro, all the indicators are showing an additional dark background. Also some indicators look way distorted (like the copyq indicator in this example)
I see a similar issue:
The Nextcloud client icon there has a white background behind it for some reason when it shouldn't.
Same for me (Gnome 41.1 with Wayland, since the latest Manjaro update)

The icons are for flameshot and copyQ
When adjusting the icon size through extension settings, some icons seem to be resized only vertically, while others are resized proportionally. I was able to get undistorted icons with size=22 on my system.
Default size:

Size=22:

Size=32 (notice how KeepassXC and Flameshot icons remain constant width):

Manjaro, Gnome 41.1, Wayland, gnome-shell-extension-appindicator 41-1
Manjaro, GNOME Shell 41.1, Wayland

When the indicators are on a panel and the panel is so short that it doesn't fit them, most of them are hidden, but the KeepassXC indicator is shown beyond the panel. That indicator is the only one that scales only vertically, not horizontally. There can be some correlation between them.

All my indicators provided by this extension are for Jetbrains Toolbox, KeepassXC and Dropbox. An image of the indicators:

To work around the white background (apparently all qt- indicators):
env XDG_CURRENT_DESKTOP=KDE flameshot
On Dash to Panel, a number of icons are invisible or shifted far to the left. Here, the icons which are normal are clickable in the spot they are in, but to click on the Nextcloud indicator, I have to click on one of the imageless buttons which exist in the large empty space to the right of the visible icons.

The five visible icons are the only ones that are supposed to be there, but in the empty space, there are 18 invisible buttons that only appear if I mouse over that area, as you can see by the faint crescent shape in the image.
Same problem here, with CopyQ and Flameshot.

System:
- os: Manjaro Linux 21.2.0
- gnome-shell: 41.1
- X.Org X Server: 1.21.1.1
Opening the application with the env var that @doppelhelix mentions fixes it, thanks for that. By the way, do you know how to make that a permanent change?
Edit:
Found a way (not sure if the right one, but worked), by editting ~/.config/autostart/copyq.desktop and ~/.config/autostart/Flameshot.desktop to include in the Exec instruction with the XDG_CURRENT_DESKTOP var:
Exec=env XDG_CURRENT_DESKTOP=KDE copyq
Exec=env XDG_CURRENT_DESKTOP=KDE flameshot
CopyQ still looks distorted though, probably related to distortions mentioned on the above comments:

Fixed after latest update on Manjaro Linux. Gnome 41.2
I've the feeling that legacy tray icon is causing this not to work properly for you...
Can you comment out TrayIconsManager.TrayIconsManager.initialize(); (and maybe TrayIconsManager.TrayIconsManager.destroy();inextension.js` and see if that fixes the issue?
In such case, I may just add an option to disable tray icons at all. Sadly it's not possible at this level to control what icon can use a tray icon and what not.