I can give you a prime example of that! A very experienced and greatly respected colleague of mine recently asserted that he thought a certain aircraft type's air data system was excellent because in the sim the numbers were "all good" even in the transonic region of the envelope. However, subsequent discussion with another colleague who was working on the real aircraft's air data system revealed that it was actually quite poor, particularly the static pressure errors which were "somewhat unpredictable".
The lesson I learnt? Never assume the sim represents the real aircraft unless you know the system or flight envelope behaviour you are seeing has been validated by data from the real thing!