I had that happen to my 302 Cobra manifold years ago.
My theory is that it was due to me not loosening the bolts (when removing the manifold) in the proper sequence. If there is just a slight warp to the upper and the outside bolts are removed last, it can put some stress on that weak point. Also if the manifold is still warm when the bolts are removed the shape of the manifold will be preloaded due to thermal expansion (thicker parts will cool slower). Another possible factor is the phenolic spacer I was using, which may have increased stress on the ear due to differing thermal expansion characteristics.
Do any of these explanations make sense to your application?
When mine broke, I did have it welded by a small time local welder, then took it to my favorite machine shop for some surfacing. I don't remember the expense, but it was worth it to preserve the manifold.
Good Luck
jason