if you are making HSTs, both pieces should be the same size. I'm not sure, but it sounds like you are making snowball blocks, with 'flippy corners'. if so, when you sew, you don't sew exactly on the line, you sew right next to the line, a bit towards the outside corner. The other thing is if the added triangle is slightly smaller, like an eighth or less, don't cut all 3 excess layers. Just cut the 2 inner layers and leave the original corner on the larger piece and use this edge when joining your blocks. The loose edges of the slightly smaller triangle will be caught between the larger piece and the adjoining patch making it secure. If you think of it, you can use a bit shorter stitch length for even more insurance.