If I was you, I would pull the interior skylight shroud. When I pulled mine because it was cracked, the factory had the ceiling panels flexed to far and cracked the skylight shroud around one of the screw holes. My guess is they flexed yours to far too. Drill a hole at the end of the crack to stop the crack. Fill with color matching caulk to fill the cracks.
I would pull that shroud though to see what is going on.