Bees fill voids greater than 3/8″ (1cm) with comb. When not given a guide to work with they build it according to their own liking. Hence the marvel of Hoffman frames and hive designs that encourage them to build within the design guidelines.
I made this mistake last year, discovered it, and left it until this year. Somehow I placed six shallow frames in a medium hive body located in the center brood box position. On inspection last year I realized my error when I tried to remove the frames. Oops! Since last summer I have spent many sleepless nights tossing and turning anxiously awaiting 2018 spring inspections when I hoped the box would be vacated and I could remove it. Yesterday was the day and last night I finally had a good night’s sleep. 🙂 BTW: These bees get an F for maintaining proper bee space.