Some roof leaks happen at step flashings.
Roof leak wall meets slop below skylight.
Skylight leaks in heavy rain are a common source for roof leaks.
Part of the flashing turns up on the wall and the other portion gets covered by the next row of shingles.
The screw holes at the laps will also start leaking.
Especially as your home ages a bit.
No matter how well your skylights were installed it is still possible for them to leak during heavy rains.
Build a corrugated roof flatter than 5 degrees it is quite common and it will overflow during heavy rain.
The laps on the roof sheets get flooded when excessive water fill the corrugations and overflow under the laps.
During installation each skylight essentially creates a big hole in an otherwise uniform roof surface.
Common causes of this type of leak are broken sprinkler pipes improper drainage from downspouts or french drains or grading that slopes toward the house.
The roof sheeting manufacturers state that the minimum slope is 5 degrees.
Sloped glazing such as roof skylights probably has historically had more leaks into the roof structure due to improper roof flashing than other window failure causes.
As each row of shingles is laid a step flashing is installed over the shingle next to the wall.
If your leak is coming through at the lower level you may have exterior below grade issues.