I have been thinking about this pin and rod issue and the only way this can happen is if the case isn't all the way in the shell holder. When this happens the one size fits all rod has enough room to let the case be far enough out of line the pins hits the case head beside the flash hole. This lets the pin hit the case head beside the flash hole.
I think Lee was hearing about this issue and came to the same conclusion.
I was browsing the Lee web site an spotted something. They came out with replacement rods for the universal decapper die that the shank looks more like the regular expander rod. The shank is larger where it enters the case. Big enough so it's close enough fit so that when the shank passes through the case neck it moves the case a bit so the case aligns better with the pin. That way the pin goes in the flash hole.
This should help prevent the pin from breaking or the rod getting bent.
At $3.50 each and in 8 sizes a person could get just the size he needs.
It may not help with flash holes off center or some of the more crimped in primers.
Just thought I'd pass this bit of info on.
Leo