This operation will not work, as you are trying to do a union to a curved surface.
To complete the operation You need a flat surface do the union, then do a bend modifier to that, to get your curve.
I'm not too sure I understand. I've boolean-subtracted spheres, cubic figures, and (lathed) objects with round surfaces from each other before, and I
don't always get the error message. In fact, to create a cresent-looking hemisphere, I subtracted a smaller circle from a bigger one, and it worked; amoung the random times it mysteriously does.
The reason I revived this thread is because, as I've consistently ran into in the past, I ran into this error message again when trying to subtract a "screw" object from my Cannon chess piece; this, to create the cannon's main body component with a hole drilled through it. Whether it's B-A or A-B, I still get this "error 3" message.
http://www.filedropper.com/transfiguringcannonandscholarintofidechesspieces (change to front view, if not already there)