If I understood your question/issue correctly - when you sew two layers together, and you think they are the same length to start with - you end up with one piece "shorter" than the other?
On many older machines the bottom layer feeds a bit faster/more than the top layer. The feed dogs grab the bottom layer and the top layer just goes along for the ride.
I think I used to compensate for that by holding the bottom layer back just a bit.
So one has to make sure that each join/intersection meets where it is supposed to.
I used to mark my strips to make sure that they were ending up where they were supposed to.