mis-manufactured parts?
I don't think it's uncommon for parts that have been mis-manufactured to have their condition re-assessed for suitability of use.
When drilling or machining so many holes, in anything to do with an aircraft, some mistakes are made; some are recoverable, and some are not.
I would assume it would be uncommon for an airplane to be delivered from manufacture without some form of manufacturing concession, or variation from an intended state (my phrase - not a manufacturers).
Holes in the wrong places are not uncommon. It's the ones without legal concessions that are the problem!