If the protocol says "(1) Check out tools before using them. (2) Check in tools when returning them. (3) Verify all tools checked out have been checked in before marking the job complete." that's one thing. Sending employees to training on how to do this and seeing daily clipboards by the tool room with initials might make you think the protocol is in use. And if there are supervisors making sure that the clipboard is full of initials at the end of the day, that can give you a nice warm fuzzy feeling.
The problem comes when supervisors want to 'look good' by having no deviations from the protocol. If people are post-dating their check-in or pre-dating their check-out, or checking stuff in that's still in use by a coworker, the protocol is less than useless.
When humans are tasked with following those protocols, they'll make human mistakes sometimes. If there are no mistakes that's not good, that's bad - it indicates the metrics are being fudged. I think any supervisor that fails to find a deviation from the protocol or who can't list an event when the protocol required action outside the norm does not look good.
Similar stuff applies to software development: If you're doing code reviews, or testing before check-in, or signing off on releases, and can't point to a time when the protocol said "nope, go back to the drawing board" you're not actually making your development safer you're making it a hassle.
It also might be downstream or upstream of the Boeing factories, like at one of the companies that manufactures major components (example: Spirit AeroSystems manufactures the 737 main fuselage and I'm told Section 41/cockpit of many aircraft) or at one of the maintenance facilities.
That same guy also said it had to do with the location of that new factory and the lack of company culture paired with managers who just had the numbers in mind.
<Interruption>
<Return to work>
You start out three step before your last step.
You repeat/check those steps.
Its time intensive as hell, which is why the usual interruption to egostroke for meddle management does rarely happen in aircraft maintenance and production.
Airbus ( and I'm sure pretty much all the other manufacturers ) has all the processes for training the workers about this problem, how to avoid it, how to deal with it when happens, check-in and checkout all the tools at the start and the end of the task, inspections, etc. this is so basic it hurts.