>how do you prevent bees from placing pollen in cut comb honey when you place
>the honey super directly above the excluder.
 
About the only way is to make sure there is a layer (even narrow) of capped
honey below the super.  The bees store pollen at the upper edge of the
brood nest, just below the honey stores. Provide your surplus room above
this layer and your combs will be full of just honey.   Once you do have a
layer of honey above the pollen, too, you probably don't need the excluder
anyway, as most queens won't cross the pollen/honey barrier to lay eggs
above.
 
Probably the way to best deal with this possibility (seasons vary) is to
leave the very first honey super above the brood chamber throughout the
flow.  In other words, don't go shifting its position, putting the next
super(s) under it.  That way any pollen stored above the brood chamber is
concentrated in that first honey super, probably in the center combs, and
you can cut around the pollen as necessary when you go to pack the honey.
(Not ideal, but much of this endeavor requires a bit of compromise.)
Actually, some folks WANT comb honey with pollen in it.
 
Alternatively, you could crush and drain the "polleny" combs over a
strainer to salvage the liquid honey in them, or run them thru an
extractor.