The only thing I can think of - you aren't getting them completely symmetrical when cutting/trimming.
I've not made this, but it looks fun! I'd start with assorted squares of fabric, then cut off the apposing corners (exactly same measure, making sure cuts are parallel and perpendicular to center) Then sew a narrow strip on the center block, and then reattach the two cut off corners. then trim using the center piece corners to square up.
If they end up not lining up - the square may not have been "square" at the start, so when cut and trimmed things don't line up, or, the cuts were not both perpendicular to the center, and parallel to each other.