Are all the simc options the same as you are doing ingame? (Flask, food, pre-pot, combat potion, same fight duration, bloodlust) Are you playing your rotation absolutely perfectly and never making the wrong decision? Simcraft should always be higher than your real life DPS (because there is no human error involved), and the difference becomes greater as more things change from the simulation. That said, some classes do have inaccurate sims or ones that don't work correctly for certain talents/legendaries so there is that too.
Also, Enhancement has a lot of RNG at play. The baseline chance for Stormbringer procs is 10%, increasing with your Mastery.. but sometimes it can proc off itself repeatedly. I had a 75 second fight where I used Stormstrike 34 times. Then I was a pug in a regular Court of Stars and managed to kill the first boss without ever getting a proc! It goes without saying the difference in damage done was massive.