I've had this error before, it's a real pain in the arse. it usually occurs when the two objects have a complicated interface boundary. Where there are two edges not quite in line with each other, or if one or other of the shapes has had lots of ops performed on it. I think in your case, some anomoly has caused the copied shape to be ever-so-slightly different to the original, and when you put them back together, they don't quite line up.
Don't know how to fix it, Ive had to either start the component again from scratch, or think of a different way to get the same effect. eg can't you slice the bit off the original? or use a separate extruded shape? You could try to offset the subtracted solid to make it noticably bigger than the other, so there are fewer coincident edges...
If this is part of a large or complex drawing, draw the part from scratch on a new dwg and import it. Sorry I can't be of any more help. :-(