Daon,
I agree with R. Johnson. When you are cutting with the torch and make a cut from one side over towards the middle, then start from the opposite side and cut back towards your first cut and it doesn't meet in a clean line. You must dress it up by grinding any notches out to prevent stress raisers from developing from the notch. Typically when coping out a flange on a beam, it takes more than one cut and the radius needs to be nice and smooth when transitioning from the first to the second cut. If the two cuts don't meet properly you should grind the cope to a nice smooth radius rather than leaving it jagged.
Hope I didn't confuse you further. Check out Figure C5.1 and C5.2 and maybe the pictures will help show what we are trying to clarify.
John Wright