Well, it's only slightly confusing
When someone says "stems" to me, i think of a subgroup of tracks, like drums or vocals, keyboards or guitars, so in this scenario, one would assume, quite rightly, that the export source would be a buss which by it's very nature is stereo.
What I think you're doing is exporting individual tracks so if can clarify exactly what you're doing then a solution will I'm sure present itself.