These are the kinds of failures you get when you try to proceduralize everything with foolproof procedures, checklists, run-books, processes, etc. The maintenance people didn't even know they were making a judgement call.
Had the technicians sleeved the offending tubes with appropriate chafing gear and secured them to reduce movement as would be common place in more earthly situations instead of trying to get it "technically in spec" without thinking about the implications of what they were actually doing this problem may very well have been averted. But maintenance people in aviation aren't really ever exercising those creative problem solving skills since it's such a book driven workflow they're always dealing with so of course they missed the forest for the trees (not that they would have been allowed to implement a one-off fix like that).