If you look closely, I think we can see the head of the skylight in both photos, if I am reading the lap of the shingles correctly.
If this is the case, then the "ears" of the flashing on each side form dams which would hold water at the head of the skylight rather than letting the water flow down and around the skylight. If the slope of the roof is shallow enough in relation to the height of the obstruction, then water could back up under the shingles or up and over the curb which looks a little short.

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Jim Luttrall
Mr. Inspector.net, Inc.
Allen, Texas 75002