I installed Freecad version 1.1 to see if I could get on with it. I have used Freecad a lot in the past but now mainly use Design spark or Solid edge.
I started to design a single cylinder simple IC engine. 25mm bore and stroke with some fillets to soften some of the edges. After drawing the cylinder I decided to section it by drawing a 26mm square on top of the cylinder and pocketing it through the cylinder to create a sectioned view. Several attempts later I realised Freecad still had problems with fillets, so I deleted them. I could then section the engine to examine the interior of the cylinder. I then pressed CTR Z to undo the section to restore the cylinder, deleted the now not needed drawing of the section square, and this happened. (see attached image).
Each time I tried to delete or alter the drawing of the square Freecad turned my round engine into a square one.
A square cylinder might just about work, but a square crankshaft? or a cam with square lobes?