It seem to be on i3 since every major DEs I have tried (Gnome, KDE, XFCE, LXQt, etc.) do not have this problem. I dug into configs but this combination does not seem to bound to anything so if anyone know where I should look into please point it out.
PS. I did test it on keyboard testing website and indeed when I hold Ctrl it seem normal but when I pressed ` it did not show that I press the ` key at all
It is quite possible that Ctrl+` is bound to showing dunst history. Check the ~/.config/dunst/dunstrc file
The line
history = ctrl+grave
binds it to dunst showing history. Remove it or change it to something else. Save the file.
Then run this in the terminal
killall dunst
notify-send foo
This will stop dunst and the notify command will again fire it up. (I don’t know a better way to reload dunst)
This should hopefully work. 
Thanks! I completely forgot about Dunst! I’ll check it as soon as I get back to my laptop!
Works like a charm. Thank you a lot
Glad to help you 
Just a little bit unrelated question. Shouln’t i3 (as a window manager) take precedence over any other application in key detection? Or is it possible to determine which application takes precedence?
Yes it should 
If i3 has a binding for the key combination, then it will execute the specific command. If it does not, then the background services, like Dunst, will catch the key press. If even then background services don’t have a command for the key press, then it finally goes to the currently focussed application.
That’s the reason why I never use key combination with ctrl or alt only in my dotfiles, since most applications use ctrl and alt for keyboard shortcuts and my wm will interfere with these applications.
Pardon me for the delay in replying. Took a break because my exams were on.