The roof edges of the hole the skylight cut may not all be angled correctly. It sounds like one edge is a very low slope. With the roof tool active, select the side of the skylight hole and set angle to perpendicular (or angle of your choice) and apply to all the edges.
Place your cursor on the hole edge so the Mercedes cursor is showing. In the pet palette, the top right button is the edge condition one. The Apply on Selected Polygon will apply the edge slope condition to all the skylight hole edges, and no other roof edges.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"