As in here where the facing gambrel's bottom rake edge meets the main house and you see the triangle of shingles? The difference I suppose is you were adding a gambrel to a standard wall, so it doesn't look normal as in the pic below.
If you do install shingles vertically make sure you at least nail them in the right place (there is sometimes a different line for steep nailing, or just make your nail placement as close a possible to being exposed when the next shingle is put on top), and it may require storm nailing (more nails). I'm pretty sure the last time I read the shingle package it also said hand seal every shingle with tar. Like that ever happens.
I agree that it generally looks hokey to have shingles where siding belongs, if that's your case.