as I have suggest on another thread generally in year 1 you don't want to use an excluder at all being the idea is to get as much comb drawn with as little impediment to this primary purpose as humanly possible. in year 2 with proper employment of a reduced bottom entry and a top entrance an excluder can 1) enhance your honey crop (the surplus is above the excluder) and 2) act as a LIMIT to swarming (by decongesting the brood nest).
I would suspect the same thing is happening as Iddee described. if so the proper manipulation is to reverse box moving the brood nest downward and the empty box upward. if the two box of deeps are a bit of this and that then reshuffling the frames is advisable.