Desktop files for apps installed in toolbox

After some minor tweaking i got audio and 3d-aceleration working inside toolbox. So i tried copying the desktop file of an app(installed inside toolbox) to ~/.local/share/applications and edited the Exec line:

Exec=toolbox run /usr/bin/chromium-browser %U

After this the app runs and works perfectly, except one minor thing. If i pin the app and then open it, two icons appear in the dash. Other apps also showed same results.
Are the WMClass of container apps somehow different than non-container ones?
(Although xprop gave the same WMClass “Chromium-browser”)

Edit: As i was writing this, i tested another app called Minetest. It does actually works but it breaks, after launching if i open overview (swooshing mouse to the top-left screen) just before the minetest window appears then two icons problem happens again. This wasn’t reproducible with chromium.
Screenshot%20from%202019-10-18%2023-25-52