i noticed this with my two. both were perfectly trained, then once bonded they were dropping stray poos, but *only* in the pen, never out during their run-time. i figured out that they were mostly centered around their hay container. i repositioned the hay container so they have to sit in the litter box to eat hay, they can’t reach it otherwise. the problem immediately corrected itself. also, once they were bonded i took out the second box and they were only using one. i don’t think they liked this, so i’ve added the second box back in.
like Sarita said, some bunnies always will drop territorial poos. the major thing is that the pee is in the box. if the stray poos are bothering you, be very diligent and pick them up as soon as you see them and toss ’em in the box. and i agree, once bonded, bunnies should not be separated unless you want to risk losing the bond and starting all over.