SPR: 547784 this is supposed to be fixed in 2016 SP5.
I had reason to recreate a part similar to one I produced before it was fixed, and sadly it is wrong still, but in different ways.
I opened it in 2018 SP2 and recreated the worst offending feature and it was still wrong.
So in some cases the error is large, can be seen on the preview. In other cases the error is small, and you only find it when subsequent features wont create or go weird.
The errors were different in my original part, but of the same nature. Whatever they did they succeeded in changing the magnitude of the problem, either worse or better depending on the scenario
I've attached the 2016 sp5 file. See if its the same for you, and on similarly non square parts.