I'm not sure if this is a bug and if there's a work around. Let me know if there is.
To replicate, make two cubes: one smaller, one larger. Add a particle system to the smaller cube. Put a Boolean modifier on the smaller cube, select the larger cube as the object in the Boolean modifier, and overlap it with the smaller cube to cut a portion of it. Check "Use Modifier Stack" so that the particle will account for the Boolean modifier and make sure the Boolean modifier is above the Particle System in the modifier stack.
Everything works as expected.
However, when you move the larger cube to completely overlap the smaller cube, something weird happens. The particles emit from the origin of the smaller cube (I set the origin to outside the cube to show it's not just emitting from the volume) despite the particles source being set to emit from faces which there are none of.