I have never had a problem with layer cakes stretching. Could it be the layer cake itself was not exactly on the straight of grain in the first place. Perhaps a light spray of starch or a similar substance might help. Give it a try on just one 9 patch.
This seems like the same old story but check you 1/4" seam allowance. Even a few threads off could make a wonky square after stitching pressing, cutting and restitching. Watch your ruler also so that it does not slide even just a little bit causing an inconsistent cut in your 9 patch.
Did you wash your squares? (I don't) That could make a difference.
Hoping someone else can give you more answers.