These lines of Wilfred Owen’s poem “Dulce et Decorum Est” refer to different things.  The first part of the line you mention refers to the glass lenses, vision ports, in the gas masks the soldiers used.  The second part of the line refers to the chlorine gas that has been fired at the soldiers in this vignette.

The first part of the line refers to the imperfect vision that the gas masks afforded the soldiers.  The masks, of course, had to have something that allowed the wearer to see out.  This glass was not necessarily perfectly clear.  In addition, as the soldier wore it, their body heat could cause it to fog up.  Thus, the “misty panes” are the pieces of glass in the gas mask that allow the narrator to look out and see his comrade who has been caught without his gas mask on.

The second part of the line refers to the chlorine gas that the Germans have fired at these soldiers.  Chlorine gas had a distinctly greenish color to it.  If enough shells full of this gas had exploded, thick clouds of the gas could have been expelled.  This would have caused the light coming through the gas to be green. 

So, the “misty panes” are the glass parts of the narrator’s gas mask and the “thick green light” is the light that has been made green and murky by passing through a cloud of chlorine gas.