What is a plausible scenario for aircraft sabotage for a science fiction novel?
If the alien has to see it to fix it, that rules out anything not visible from the windows (i.e., tail, landing gear, etc.)

If the alien is a passenger, the only moving parts that come to mind are the ailerons.

Have your saboteurs cause a complete failure of the aileron controls (In a Gulfstream 3 I think it's cables with a hydraulic boost, but I could be wrong).  A semi-cut cable won't be caught on a preflight (who takes apart a wing?), but could break over the ocean.   

Your alien could save the day by directly manipulating one of the ailerons to keep the plane level.

I don't know the forces involved - I hope your alien is really strong.