Hate to tell you with, but speaking as an Engineer who has certified several complete aircraft, and lots and lots of modified aircraft - there probably isn't an aircraft flying which meets every bit of the design code it was certified against.
It just isn't possible, that's why the people who approve new aircraft designs have large salaries and grey hair. The art of certification is churning out an aeroplane that's as close as you can get it, and all non-compliances have been shown "acceptable". Sometimes we get this last bit wrong, I've not worked on Concorde or the 747, but I can think of a number of aircraft where these assumptions were made and they came back to bite us - but far more where thank goodness they didn't.
What is very very important, is that the deficiencies are documented properly and everybody involved in operating the type is aware of them.
G