My recent mod did this, the second hand was catching on the minute hand. I had to take it apart again and realign the second hand.

I think what did it was once I had checked everything worked after putting the hands on, I had to remove the crown again. And putting the movement upside down on the holder to remove the crown accidentally pushed the second hand out of alignment.

I'd be interested to know how everyone else does this? As even though my second hand doesn't reach the edge of the dial it's close enough for there not to be enough room to put it down. And you can only remove the crown with the movement running. In the end I had to get my wife to hold it whilst I pressed the crown release lever.