I strongly doubt that the bolt had anything to do with the bottom bracket's failure, which was most likely weather or dirt related. The bearings are well outboard of the damaged center section who's sole purpose is as a spacer between the two bearings.
That said, thread the bolt back into the open BB shell, and gauge how far in it extends, then file or grind it shorter, so it just enters the shell the slightest bit (or buy a shorter bolt).
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