Crashes due to out-of-limit CG conditions are (unfortunately) not uncommon in small, privately owned aircraft, but very rare in commercial operations.
There was Air Midwest 5481 back in 2003.
ASN Aircraft accident Beechcraft 1900D N233YV Charlotte-Douglas International Airport, NC (CLT)
However, that was on take-off and needed more holes in the cheese than just a CG a bit aft of the limit.