If you are using Illustrator’s Pathfinder tool and you find that shapes are having their points mangled whenever you apply shape modes or pathfinders, realize this: the Pathfinder uses a ‘precision’ setting that rounds out your shapes. This precision is relative to the absolute measurement of points, so small shapes will get visually distorted while larger ones seem perfectly fine.
What’s the solution? Scale things up before you apply the Pathfinder, then scale them back down again. Make sure that Pathfinder hasn’t automatically checked the ‘align to pixel grid’ box on your edited shapes or you will find it distorting again once they return to a small size.