EnergyPlus doesn't have "Skylights", only Fenestration components.
This is merely an OpenStudio object, by default if you draw a window on an horizontal surface it'll be recognize as a Skylight. That allows you in turn to specify a default construction object for those Skylights that is different from the regular Windows.
I suspect your error comes from the fact that you don't have a default Skylight construction defined and therefore after translation to EnergyPlus input file you end up with a FenestrationSurface:Detailed
of type Surface TypeWindow
that has no construction, and E+ crashes.
On the "Constructions" tab, here showing the default "189.1-2001 - Office" construction set:
What's your error...?