I'm kind of a "picky" guy [pun intended] - I presume from your description the parts are similar in configuration and size.
Procedures are clear, employee is more than adequately trained... I can find no hole in the process... he simply grabbed the wrong part... instead of grabbing 6 pieces of part ABC, he grabbed 6 pieces of part BCD which are very close in size to part ABC.
Maybe the part numbers are also similar.
Do you have many parts similar in size and configuration? Are they in bins close to each other? Do you have a mistake proofing process (other than counting on a super alert order picker?)
Having been the idiot who pulled a dozen 3-inch lag bolts from the local self-service hardware store when I really wanted 3-1/2 inch bolts, I can empathize with the order picker, especially after I got up on the ladder and put the first bolt in, only to find it too short.
Despite the apparent small cost of the error, the real cost is in the soft costs of handling the error and the loss of confidence from a customer who expects perfection.
If it were my operation, I'd relook at my inventory layout and see if there were other opportunities for mistakes.
When I returned to my hardware for the correct bolts, I made one small suggestion they adopted the same afternoon - they put up laminated rulers and gages on each shelf of screws and bolts and nuts for customers and clerks to check on the spot without having to search around for a measuring instrument. (Incidentally it cut down on folks putting parts back in the wrong bins.)