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