A gap in the roof?

Sylvia, a homeowner in California, asked: 

There is a large noticeable gap between skylight and roof tiles after roofer finished replacing broken tiles for maintenance work. The roofer says it's fine because there is flashing underneath but I disagree. What can it be done?

Martin Stout with Go Roof Tune Up shared:

Properly installed skylights have flashings around the roof to curb connection. Head flashing at the bottom of the skylight that goes on of the top of the tile below, Pan flashing that go along both sides of the skylight under the tiles and Saddle flashing that goes at the top of the skylight and under the tile above. This creates a cascading for the water to stay on top of the tile. The photo appears to show a factory made skylight/curb unit. These types of skylight normally have the flashing detail built in to factory curb. 

The gap left will allow water to flow and help keep debris from building up. Photos of the bottom of the skylight would help confirm proper installation. 

Carlos Rodriguez at Mr. Roofing, says:

If the flashing was installed correctly, the skylight and roof should be watertight. From the picture you shared, it appears to be a Velux deck-mounted skylight. Proper underlayment and flashing should integrate the skylight with the existing roof system.  

The gap mentioned is due to the deck-mounted skylight being flush with the roof substrate, while the tiles sit on a batten system. The other penetrations on the roof should have similar gaps where the flashing for those penetrations interface with the tile. If there is any uncertainty, seeking a second opinion from a roofing professional can provide additional assurance.